From 0146246144cfc3ef9f186e3f6b67f766057d8b62 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:33:05 -0400
Subject: [PATCH 01/28] feat(config): add sync _find_project_root helper

---
 src/pythinker_code/config.py | 17 +++++++++++++++++
 tests/core/test_config.py    | 19 +++++++++++++++++++
 2 files changed, 36 insertions(+)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index e2c65cdf..414eebc6 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -30,6 +30,23 @@
 from pythinker_code.share import get_share_dir
 from pythinker_code.utils.logging import logger
 
+
+def _find_project_root(cwd: Path) -> Path | None:
+    """Walk up from cwd to find the nearest directory containing .git/.
+
+    Returns None when no .git marker is found before reaching the filesystem
+    root, so callers can skip project/local scopes without a fallback.
+    """
+    current = cwd.resolve()
+    while True:
+        if (current / ".git").exists():
+            return current
+        parent = current.parent
+        if parent == current:
+            return None
+        current = parent
+
+
 AgentExecutionProfile = Literal[
     "default",
     "review_safe",
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index cf7e9d03..3f6ecf9a 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -5,6 +5,7 @@
 
 from pythinker_code.config import (
     Config,
+    _find_project_root,
     get_default_config,
     load_config,
     load_config_from_string,
@@ -258,3 +259,21 @@ def test_load_config_compaction_trigger_ratio_too_high():
 def test_auto_deliberate_is_a_valid_policy() -> None:
     c = Config(ask_user_question_policy="auto_deliberate")
     assert c.ask_user_question_policy == "auto_deliberate"
+
+
+def test_find_project_root_finds_git_root(tmp_path):
+    git_dir = tmp_path / ".git"
+    git_dir.mkdir()
+    subdir = tmp_path / "src" / "pkg"
+    subdir.mkdir(parents=True)
+    assert _find_project_root(subdir) == tmp_path
+
+
+def test_find_project_root_returns_none_outside_git(tmp_path):
+    # tmp_path itself has no .git ancestor in practice
+    assert _find_project_root(tmp_path) is None
+
+
+def test_find_project_root_finds_root_in_cwd(tmp_path):
+    (tmp_path / ".git").mkdir()
+    assert _find_project_root(tmp_path) == tmp_path

From 0431f01599c4322639c1087a218ccfe1a3e9badc Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:35:07 -0400
Subject: [PATCH 02/28] feat(utils): add ensure_gitignored utility

---
 src/pythinker_code/utils/gitignore.py | 30 ++++++++++++++++
 tests/utils/test_gitignore.py         | 50 +++++++++++++++++++++++++++
 2 files changed, 80 insertions(+)
 create mode 100644 src/pythinker_code/utils/gitignore.py
 create mode 100644 tests/utils/test_gitignore.py

diff --git a/src/pythinker_code/utils/gitignore.py b/src/pythinker_code/utils/gitignore.py
new file mode 100644
index 00000000..3918f125
--- /dev/null
+++ b/src/pythinker_code/utils/gitignore.py
@@ -0,0 +1,30 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+
+def ensure_gitignored(git_root: Path, pattern: str, comment: str = "") -> None:
+    """Append *pattern* to <git_root>/.gitignore if not already present.
+
+    Creates .gitignore if the file does not exist. Handles missing trailing
+    newline before appending. Prepends a comment line when *comment* is given.
+    """
+    gi_path = git_root / ".gitignore"
+
+    if gi_path.exists():
+        content = gi_path.read_text(encoding="utf-8")
+        # Check if pattern is already present as a standalone line
+        if any(line.strip() == pattern for line in content.splitlines()):
+            return
+    else:
+        content = ""
+
+    lines_to_append: list[str] = []
+    if content and not content.endswith("\n"):
+        lines_to_append.append("\n")
+    if comment:
+        lines_to_append.append(f"# {comment}\n")
+    lines_to_append.append(f"{pattern}\n")
+
+    with gi_path.open("a", encoding="utf-8") as f:
+        f.write("".join(lines_to_append))
diff --git a/tests/utils/test_gitignore.py b/tests/utils/test_gitignore.py
new file mode 100644
index 00000000..789697f3
--- /dev/null
+++ b/tests/utils/test_gitignore.py
@@ -0,0 +1,50 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+
+from pythinker_code.utils.gitignore import ensure_gitignored
+
+
+def test_creates_gitignore_when_absent(tmp_path):
+    ensure_gitignored(tmp_path, ".pythinker/config.local.toml", comment="Added by pythinker")
+    gi = tmp_path / ".gitignore"
+    assert gi.exists()
+    content = gi.read_text()
+    assert ".pythinker/config.local.toml" in content
+    assert "Added by pythinker" in content
+
+
+def test_appends_to_existing_gitignore(tmp_path):
+    gi = tmp_path / ".gitignore"
+    gi.write_text("*.pyc\n", encoding="utf-8")
+    ensure_gitignored(tmp_path, ".pythinker/config.local.toml")
+    content = gi.read_text()
+    assert "*.pyc" in content
+    assert ".pythinker/config.local.toml" in content
+
+
+def test_no_op_when_pattern_already_present(tmp_path):
+    gi = tmp_path / ".gitignore"
+    gi.write_text(".pythinker/config.local.toml\n", encoding="utf-8")
+    ensure_gitignored(tmp_path, ".pythinker/config.local.toml")
+    # No duplicate
+    lines = [l for l in gi.read_text().splitlines() if l == ".pythinker/config.local.toml"]
+    assert len(lines) == 1
+
+
+def test_fixes_missing_trailing_newline(tmp_path):
+    gi = tmp_path / ".gitignore"
+    gi.write_text("*.pyc", encoding="utf-8")  # no trailing newline
+    ensure_gitignored(tmp_path, ".pythinker/config.local.toml")
+    content = gi.read_text()
+    # Pattern must start on its own line, not appended to "*.pyc"
+    assert "\n.pythinker/config.local.toml" in content
+
+
+def test_omits_comment_when_empty(tmp_path):
+    ensure_gitignored(tmp_path, ".pythinker/config.local.toml", comment="")
+    content = (tmp_path / ".gitignore").read_text()
+    assert ".pythinker/config.local.toml" in content
+    assert "#" not in content

From a79310fde0498211ac218d5a97ec9eea71e7e7ef Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:38:00 -0400
Subject: [PATCH 03/28] fix(tests): remove unused imports and rename ambiguous
 variable in test_gitignore

---
 tests/utils/test_gitignore.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/tests/utils/test_gitignore.py b/tests/utils/test_gitignore.py
index 789697f3..d1353b58 100644
--- a/tests/utils/test_gitignore.py
+++ b/tests/utils/test_gitignore.py
@@ -1,9 +1,5 @@
 from __future__ import annotations
 
-from pathlib import Path
-
-import pytest
-
 from pythinker_code.utils.gitignore import ensure_gitignored
 
 
@@ -30,7 +26,7 @@ def test_no_op_when_pattern_already_present(tmp_path):
     gi.write_text(".pythinker/config.local.toml\n", encoding="utf-8")
     ensure_gitignored(tmp_path, ".pythinker/config.local.toml")
     # No duplicate
-    lines = [l for l in gi.read_text().splitlines() if l == ".pythinker/config.local.toml"]
+    lines = [line for line in gi.read_text().splitlines() if line == ".pythinker/config.local.toml"]
     assert len(lines) == 1
 
 

From cf775ad1637c45d1e2edb512b553b5dd658a347e Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:39:26 -0400
Subject: [PATCH 04/28] feat(config): add scope constants and provenance
 helpers

Add SCOPE_LOCKED_PATHS, DEDUP_LIST_FIELDS, ENV_FIELD_MAP constants
and _set_nested, _lookup_provenance helper functions to support the
scoped config pipeline. These pure functions handle nested dict
operations and provenance tracking across config scopes.
---
 src/pythinker_code/config.py | 66 ++++++++++++++++++++++++++++++++++++
 tests/core/test_config.py    | 53 +++++++++++++++++++++++++++++
 2 files changed, 119 insertions(+)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index 414eebc6..7095603e 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -47,6 +47,72 @@ def _find_project_root(cwd: Path) -> Path | None:
         current = parent
 
 
+# ---------------------------------------------------------------------------
+# Scope system constants
+# ---------------------------------------------------------------------------
+
+SCOPE_LOCKED_PATHS: frozenset[tuple[str, ...]] = frozenset(
+    {
+        ("providers",),  # contains api_key per provider — must stay in user scope
+        ("services",),  # contains api_key fields — must stay in user scope
+        ("feedback", "api_key"),  # only the key, not the whole feedback section
+    }
+)
+
+DEDUP_LIST_FIELDS: frozenset[str] = frozenset({"allowed_domains", "extra_skill_dirs"})
+
+ENV_FIELD_MAP: dict[str, tuple[str, ...]] = {
+    "PYTHINKER_DEFAULT_MODEL": ("default_model",),
+    "PYTHINKER_DEFAULT_THINKING": ("default_thinking",),
+    "PYTHINKER_DEFAULT_THINKING_EFFORT": ("default_thinking_effort",),
+    "PYTHINKER_AGENT_EXECUTION_PROFILE": ("agent_execution_profile",),
+    "PYTHINKER_DEFAULT_YOLO": ("default_yolo",),
+    "PYTHINKER_ASK_USER_QUESTION_POLICY": ("ask_user_question_policy",),
+    "PYTHINKER_AUTO_DELIBERATE_DESTRUCTIVE_ACTIONS": ("auto_deliberate_destructive_actions",),
+    "PYTHINKER_SKIP_AUTO_PROMPT_INJECTION": ("skip_auto_prompt_injection",),
+    "PYTHINKER_DEFAULT_PLAN_MODE": ("default_plan_mode",),
+    "PYTHINKER_DEFAULT_EDITOR": ("default_editor",),
+    "PYTHINKER_THEME": ("theme",),
+    "PYTHINKER_SHOW_THINKING_STREAM": ("show_thinking_stream",),
+    "PYTHINKER_PREVENT_IDLE_SLEEP": ("prevent_idle_sleep",),
+    "PYTHINKER_TELEMETRY": ("telemetry",),
+    "PYTHINKER_SESSION_RETENTION_DAYS": ("session_retention_days",),
+    "PYTHINKER_MERGE_ALL_AVAILABLE_SKILLS": ("merge_all_available_skills",),
+}
+
+
+# ---------------------------------------------------------------------------
+# Pipeline helpers
+# ---------------------------------------------------------------------------
+
+
+def _set_nested(d: dict, path: tuple[str, ...], value: object) -> None:
+    """Walk *path* into *d*, creating intermediate dicts, then set the leaf."""
+    node = d
+    for part in path[:-1]:
+        if part not in node or not isinstance(node[part], dict):
+            node[part] = {}
+        node = node[part]
+    node[path[-1]] = value
+
+
+def _lookup_provenance(prov: "dict | str", loc: tuple) -> str:
+    """Recursively follow *loc* through the provenance map.
+
+    Integer elements (Pydantic list indices) are skipped — we map them back
+    to the parent collection's scope string so error messages stay useful.
+    Returns "unknown scope" when the path cannot be fully resolved.
+    """
+    if not loc or isinstance(prov, str):
+        return prov if isinstance(prov, str) else "unknown scope"
+    head, *tail = loc
+    if isinstance(head, int):
+        return prov if isinstance(prov, str) else _lookup_provenance(prov, tuple(tail))
+    if isinstance(prov, dict) and head in prov:
+        return _lookup_provenance(prov[head], tuple(tail))
+    return "unknown scope"
+
+
 AgentExecutionProfile = Literal[
     "default",
     "review_safe",
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index 3f6ecf9a..569fc8a8 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -6,6 +6,8 @@
 from pythinker_code.config import (
     Config,
     _find_project_root,
+    _lookup_provenance,
+    _set_nested,
     get_default_config,
     load_config,
     load_config_from_string,
@@ -277,3 +279,54 @@ def test_find_project_root_returns_none_outside_git(tmp_path):
 def test_find_project_root_finds_root_in_cwd(tmp_path):
     (tmp_path / ".git").mkdir()
     assert _find_project_root(tmp_path) == tmp_path
+
+
+def test_set_nested_flat():
+    d: dict = {}
+    _set_nested(d, ("theme",), "light")
+    assert d == {"theme": "light"}
+
+
+def test_set_nested_deep():
+    d: dict = {}
+    _set_nested(d, ("tui", "style"), "card")
+    assert d == {"tui": {"style": "card"}}
+
+
+def test_set_nested_overwrites_existing():
+    d = {"tui": {"style": "pythinker", "smooth_streaming": True}}
+    _set_nested(d, ("tui", "style"), "card")
+    assert d["tui"]["style"] == "card"
+    assert d["tui"]["smooth_streaming"] is True  # sibling preserved
+
+
+def test_lookup_provenance_scalar():
+    prov = {"theme": ".pythinker/config.local.toml"}
+    assert _lookup_provenance(prov, ("theme",)) == ".pythinker/config.local.toml"
+
+
+def test_lookup_provenance_nested():
+    prov = {"tui": {"style": ".pythinker/config.toml"}}
+    assert _lookup_provenance(prov, ("tui", "style")) == ".pythinker/config.toml"
+
+
+def test_lookup_provenance_list_index():
+    # Pydantic gives loc=("hooks", 0, "command") for a bad list element.
+    # Should return the collection scope, not crash.
+    prov = {"hooks": "~/.pythinker/config.toml+.pythinker/config.toml"}
+    assert _lookup_provenance(prov, ("hooks", 0, "command")) == "~/.pythinker/config.toml+.pythinker/config.toml"
+
+
+def test_lookup_provenance_partial_path():
+    prov = {"tui": {"style": ".pythinker/config.toml"}}
+    assert _lookup_provenance(prov, ("tui", "nonexistent")) == "unknown scope"
+
+
+def test_lookup_provenance_empty_loc():
+    prov = "~/.pythinker/config.toml"
+    assert _lookup_provenance(prov, ()) == "~/.pythinker/config.toml"
+
+
+def test_lookup_provenance_unknown():
+    prov: dict = {}
+    assert _lookup_provenance(prov, ("missing_key",)) == "unknown scope"

From 50f292cc0f9247b4a680f4a419d66ce59dbbcc15 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:42:02 -0400
Subject: [PATCH 05/28] style(config): unquote union type annotation in
 _lookup_provenance

---
 src/pythinker_code/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index 7095603e..558f7459 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -96,7 +96,7 @@ def _set_nested(d: dict, path: tuple[str, ...], value: object) -> None:
     node[path[-1]] = value
 
 
-def _lookup_provenance(prov: "dict | str", loc: tuple) -> str:
+def _lookup_provenance(prov: dict | str, loc: tuple) -> str:
     """Recursively follow *loc* through the provenance map.
 
     Integer elements (Pydantic list indices) are skipped — we map them back

From 8b785745aae535dc505f6788188e12512346e5cd Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:44:36 -0400
Subject: [PATCH 06/28] feat(config): add _check_scope_locks with path-level
 secret detection

---
 src/pythinker_code/config.py | 28 ++++++++++++++++++++++++++++
 tests/core/test_config.py    | 35 +++++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index 558f7459..b081a005 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -113,6 +113,34 @@ def _lookup_provenance(prov: dict | str, loc: tuple) -> str:
     return "unknown scope"
 
 
+def _check_scope_locks(scope_dict: dict, scope_name: str) -> None:
+    """Raise ConfigError if *scope_dict* contains any scope-locked field paths.
+
+    Checks every path in SCOPE_LOCKED_PATHS by walking the raw dict before
+    Pydantic validation, so secrets are blocked before they can be merged.
+    """
+    for path in SCOPE_LOCKED_PATHS:
+        node: object = scope_dict
+        for part in path:
+            if not isinstance(node, dict) or part not in node:
+                break
+            node = node[part]
+        else:
+            field_path = ".".join(path)
+            # Derive a short scope label for the error message
+            if "local" in scope_name:
+                scope_label = "local scope"
+            elif "project" in scope_name or scope_name.startswith(".pythinker"):
+                scope_label = "project scope"
+            else:
+                scope_label = scope_name
+            raise ConfigError(
+                f"'{field_path}' cannot be set in {scope_name} ({scope_label}).\n"
+                f"  Move it to ~/.pythinker/config.toml or set the corresponding "
+                f"PYTHINKER_* environment variable."
+            )
+
+
 AgentExecutionProfile = Literal[
     "default",
     "review_safe",
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index 569fc8a8..52c0ae62 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -5,6 +5,7 @@
 
 from pythinker_code.config import (
     Config,
+    _check_scope_locks,
     _find_project_root,
     _lookup_provenance,
     _set_nested,
@@ -330,3 +331,37 @@ def test_lookup_provenance_empty_loc():
 def test_lookup_provenance_unknown():
     prov: dict = {}
     assert _lookup_provenance(prov, ("missing_key",)) == "unknown scope"
+
+
+def test_scope_lock_providers_in_project():
+    with pytest.raises(ConfigError, match="'providers'.*project scope"):
+        _check_scope_locks({"providers": {"openai": {}}}, ".pythinker/config.toml")
+
+
+def test_scope_lock_services_in_local():
+    with pytest.raises(ConfigError, match="'services'.*local scope"):
+        _check_scope_locks({"services": {"pythinker_ai_search": {}}}, ".pythinker/config.local.toml")
+
+
+def test_scope_lock_feedback_api_key():
+    with pytest.raises(ConfigError, match="'feedback.api_key'"):
+        _check_scope_locks(
+            {"feedback": {"api_key": "secret"}}, ".pythinker/config.toml"
+        )
+
+
+def test_scope_lock_feedback_url_allowed():
+    # feedback.endpoint_url is NOT locked — should not raise
+    _check_scope_locks(
+        {"feedback": {"endpoint_url": "https://internal.example.com"}},
+        ".pythinker/config.toml",
+    )
+
+
+def test_scope_lock_clean_dict():
+    _check_scope_locks({"theme": "light", "default_model": "gpt-4"}, ".pythinker/config.toml")
+
+
+def test_scope_lock_error_mentions_env_var():
+    with pytest.raises(ConfigError, match="PYTHINKER_"):
+        _check_scope_locks({"providers": {}}, ".pythinker/config.toml")

From 6c54bd465d4b81cba35a63b70459f3c4a69fd38e Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:47:53 -0400
Subject: [PATCH 07/28] feat(config): add _type_based_merge with dedup and
 provenance tracking

---
 src/pythinker_code/config.py | 40 +++++++++++++++++++++
 tests/core/test_config.py    | 68 ++++++++++++++++++++++++++++++++++++
 2 files changed, 108 insertions(+)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index b081a005..737f6c72 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -141,6 +141,46 @@ def _check_scope_locks(scope_dict: dict, scope_name: str) -> None:
             )
 
 
+def _type_based_merge(base: dict, overlay: dict, provenance: dict, scope: str) -> dict:
+    """Merge *overlay* into *base* using type-based rules, tracking provenance.
+
+    Rules:
+    - Scalar (str/bool/int/float/None): overlay wins, provenance records scope.
+    - List: base + overlay concatenated; DEDUP_LIST_FIELDS deduplicated
+      (order-preserving, first occurrence wins).
+    - Dict: recurse so nested keys can be independently overridden.
+
+    Mutates *base* and *provenance* in place; also returns *base* for chaining.
+    """
+    for key, value in overlay.items():
+        if isinstance(value, dict):
+            # For dicts, always recurse to track individual nested keys
+            if key not in base:
+                base[key] = {}
+            if key not in provenance or not isinstance(provenance[key], dict):
+                provenance[key] = {}
+            _type_based_merge(
+                base[key],
+                value,
+                provenance[key],
+                scope,
+            )
+        elif key not in base:
+            base[key] = value
+            provenance[key] = scope
+        elif isinstance(value, list) and isinstance(base[key], list):
+            combined = base[key] + value
+            if key in DEDUP_LIST_FIELDS:
+                combined = list(dict.fromkeys(combined))
+            base[key] = combined
+            existing = provenance.get(key)
+            provenance[key] = f"{existing}+{scope}" if existing else scope
+        else:
+            base[key] = value
+            provenance[key] = scope
+    return base
+
+
 AgentExecutionProfile = Literal[
     "default",
     "review_safe",
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index 52c0ae62..a48dba21 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -9,6 +9,7 @@
     _find_project_root,
     _lookup_provenance,
     _set_nested,
+    _type_based_merge,
     get_default_config,
     load_config,
     load_config_from_string,
@@ -365,3 +366,70 @@ def test_scope_lock_clean_dict():
 def test_scope_lock_error_mentions_env_var():
     with pytest.raises(ConfigError, match="PYTHINKER_"):
         _check_scope_locks({"providers": {}}, ".pythinker/config.toml")
+
+
+def test_merge_scalar_override():
+    prov: dict = {}
+    result = _type_based_merge({"theme": "dark"}, {"theme": "light"}, prov, ".pythinker/config.local.toml")
+    assert result["theme"] == "light"
+    assert prov["theme"] == ".pythinker/config.local.toml"
+
+
+def test_merge_scalar_three_scopes():
+    prov: dict = {}
+    base = _type_based_merge({}, {"theme": "dark"}, prov, "~/.pythinker/config.toml")
+    base = _type_based_merge(base, {"theme": "solarized"}, prov, ".pythinker/config.toml")
+    base = _type_based_merge(base, {"theme": "light"}, prov, ".pythinker/config.local.toml")
+    assert base["theme"] == "light"
+    assert prov["theme"] == ".pythinker/config.local.toml"
+
+
+def test_merge_list_concat():
+    prov: dict = {}
+    base = _type_based_merge({}, {"hooks": [{"event": "Stop", "command": "a"}]}, prov, "~/.pythinker/config.toml")
+    base = _type_based_merge(base, {"hooks": [{"event": "Stop", "command": "b"}]}, prov, ".pythinker/config.toml")
+    assert len(base["hooks"]) == 2
+    assert base["hooks"][0]["command"] == "a"
+    assert base["hooks"][1]["command"] == "b"
+
+
+def test_merge_list_concat_provenance():
+    prov: dict = {}
+    base = _type_based_merge({}, {"hooks": []}, prov, "~/.pythinker/config.toml")
+    base = _type_based_merge(base, {"hooks": []}, prov, ".pythinker/config.toml")
+    assert prov["hooks"] == "~/.pythinker/config.toml+.pythinker/config.toml"
+
+
+def test_merge_list_base_case_provenance():
+    prov: dict = {}
+    _type_based_merge({}, {"hooks": []}, prov, "~/.pythinker/config.toml")
+    assert prov["hooks"] == "~/.pythinker/config.toml"
+
+
+def test_merge_list_dedup_extra_skill_dirs():
+    prov: dict = {}
+    base = _type_based_merge({}, {"extra_skill_dirs": ["/a", "/b"]}, prov, "~/.pythinker/config.toml")
+    base = _type_based_merge(base, {"extra_skill_dirs": ["/b", "/c"]}, prov, ".pythinker/config.toml")
+    # /b appears in both — should appear only once (first occurrence kept)
+    assert base["extra_skill_dirs"] == ["/a", "/b", "/c"]
+
+
+def test_merge_dict_deep():
+    prov: dict = {}
+    base = _type_based_merge(
+        {}, {"tui": {"style": "pythinker", "smooth_streaming": True}}, prov, "~/.pythinker/config.toml"
+    )
+    base = _type_based_merge(
+        base, {"tui": {"style": "card"}}, prov, ".pythinker/config.toml"
+    )
+    assert base["tui"]["style"] == "card"
+    assert base["tui"]["smooth_streaming"] is True  # sibling preserved
+    assert prov["tui"]["style"] == ".pythinker/config.toml"
+    assert prov["tui"]["smooth_streaming"] == "~/.pythinker/config.toml"
+
+
+def test_merge_key_only_in_overlay():
+    prov: dict = {}
+    result = _type_based_merge({}, {"theme": "dark"}, prov, "~/.pythinker/config.toml")
+    assert result["theme"] == "dark"
+    assert prov["theme"] == "~/.pythinker/config.toml"

From 138cab858991ae12aeed813e18f7ebeae05f6e93 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:53:11 -0400
Subject: [PATCH 08/28] feat(config): add _apply_env_vars with ENV_FIELD_MAP

---
 src/pythinker_code/config.py | 14 ++++++++++++++
 tests/core/test_config.py    | 37 ++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index 737f6c72..f464440b 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -181,6 +181,20 @@ def _type_based_merge(base: dict, overlay: dict, provenance: dict, scope: str) -
     return base
 
 
+def _apply_env_vars(merged: dict, provenance: dict) -> None:
+    """Overlay PYTHINKER_* env vars onto *merged*, updating *provenance*.
+
+    Values are stored as raw strings; Pydantic coerces them during
+    model_validate(). Only keys in ENV_FIELD_MAP are recognised; all others
+    are silently ignored.
+    """
+    for env_key, path in ENV_FIELD_MAP.items():
+        value = os.environ.get(env_key)
+        if value is not None:
+            _set_nested(merged, path, value)
+            _set_nested(provenance, path, f"env {env_key}")
+
+
 AgentExecutionProfile = Literal[
     "default",
     "review_safe",
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index a48dba21..ea1649bb 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -5,6 +5,7 @@
 
 from pythinker_code.config import (
     Config,
+    _apply_env_vars,
     _check_scope_locks,
     _find_project_root,
     _lookup_provenance,
@@ -433,3 +434,39 @@ def test_merge_key_only_in_overlay():
     result = _type_based_merge({}, {"theme": "dark"}, prov, "~/.pythinker/config.toml")
     assert result["theme"] == "dark"
     assert prov["theme"] == "~/.pythinker/config.toml"
+
+
+def test_apply_env_vars_known_key(monkeypatch):
+    monkeypatch.setenv("PYTHINKER_THEME", "light")
+    merged: dict = {}
+    prov: dict = {}
+    _apply_env_vars(merged, prov)
+    assert merged["theme"] == "light"
+    assert prov["theme"] == "env PYTHINKER_THEME"
+
+
+def test_apply_env_vars_unknown_key_ignored(monkeypatch):
+    monkeypatch.setenv("PYTHINKER_XYZZY_UNKNOWN", "whatever")
+    merged: dict = {}
+    prov: dict = {}
+    _apply_env_vars(merged, prov)
+    assert "xyzzy_unknown" not in merged
+
+
+def test_apply_env_vars_bool_coercion(monkeypatch):
+    monkeypatch.setenv("PYTHINKER_DEFAULT_YOLO", "true")
+    merged: dict = {}
+    prov: dict = {}
+    _apply_env_vars(merged, prov)
+    # Stored as string; Pydantic coerces during model_validate
+    assert merged["default_yolo"] == "true"
+    assert prov["default_yolo"] == "env PYTHINKER_DEFAULT_YOLO"
+
+
+def test_apply_env_vars_overrides_existing(monkeypatch):
+    monkeypatch.setenv("PYTHINKER_THEME", "light")
+    merged = {"theme": "dark"}
+    prov = {"theme": "~/.pythinker/config.toml"}
+    _apply_env_vars(merged, prov)
+    assert merged["theme"] == "light"
+    assert prov["theme"] == "env PYTHINKER_THEME"

From 19dde249982eb7f4c14c75de1cb3bb799079f25b Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 14:56:10 -0400
Subject: [PATCH 09/28] feat(config): add source_scopes metadata field to
 Config

---
 src/pythinker_code/config.py |  8 ++++++++
 tests/core/test_config.py    | 11 +++++++++++
 2 files changed, 19 insertions(+)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index f464440b..c481986d 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -549,6 +549,14 @@ class Config(BaseModel):
         description="Path to the loaded config file. None when loaded from --config text.",
         exclude=True,
     )
+    source_scopes: dict[str, Path] = Field(
+        default_factory=dict,
+        description=(
+            "Paths of config files that contributed to this resolved config, keyed by scope name. "
+            "e.g. {'user': Path('~/.pythinker/config.toml'), 'project': Path('.pythinker/config.toml')}."
+        ),
+        exclude=True,
+    )
     default_model: str = Field(default="", description="Default model to use")
     default_thinking: bool = Field(default=False, description="Default thinking mode")
     default_thinking_effort: ThinkingEffort | None = Field(
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index ea1649bb..509d6fb9 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -101,6 +101,17 @@ def test_default_config_dump():
     )
 
 
+def test_config_source_scopes_default_empty():
+    config = get_default_config()
+    assert config.source_scopes == {}
+
+
+def test_config_source_scopes_not_in_dump():
+    config = get_default_config()
+    dumped = config.model_dump()
+    assert "source_scopes" not in dumped
+
+
 def test_load_config_text_toml():
     config = load_config_from_string('default_model = ""\n')
     assert config == get_default_config()

From 84d2baaa3c4214843fa47bb2da2a05fd3a995f86 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 15:10:48 -0400
Subject: [PATCH 10/28] feat(config): add _load_scoped five-step pipeline
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Implements _load_scoped(project_root) as the core scoped config
resolution pipeline: Ingest → Guard → Merge → Env → Validate.

Reads user, project (.pythinker/config.toml), and local
(.pythinker/config.local.toml) scopes; enforces scope locks before
merge; overlays env vars last; attributes validation errors to their
source scope; populates source_scopes on the returned Config and
auto-gitignores config.local.toml when present.

Also wraps the Task-7 source_scopes description to fix a pre-existing
ruff E501 violation (blocked the ruff gate).

Adds 8 integration tests covering user-only, project-overrides-user,
local-overrides-project, hook concatenation, scope-lock violation,
validation error attribution, env override, and source_scopes metadata.

Note: 3 provided tests used "solarized" as a theme value, which is not
in Literal["dark","light"] and fails Pydantic validation. Tests were
corrected to "light"/"dark" while preserving their override-precedence
intent. The merge-layer three-scope ordering is independently covered by
test_merge_scalar_three_scopes.

Pyright debt: 60 errors (45 pre-existing bare-dict annotations in
Tasks 3-6 helpers + 15 same-class cascades from _load_scoped). No real
type mismatches. Deferred to Task 9 typing sweep.
---
 src/pythinker_code/config.py |  92 ++++++++++++++++++++++-
 tests/core/test_config.py    | 142 +++++++++++++++++++++++++++++++----
 2 files changed, 219 insertions(+), 15 deletions(-)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index c481986d..a2e13bd9 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -195,6 +195,95 @@ def _apply_env_vars(merged: dict, provenance: dict) -> None:
             _set_nested(provenance, path, f"env {env_key}")
 
 
+def _load_scoped(project_root: Path | None) -> Config:
+    """Run the five-step scoped config resolution pipeline.
+
+    Steps: Ingest → Guard → Merge → Env → Validate.
+    Returns a fully-validated Config with source_scopes populated.
+    """
+    from pythinker_code.utils.gitignore import ensure_gitignored
+
+    # ── INGEST ────────────────────────────────────────────────────────────
+    default_user_file = get_config_file().expanduser().resolve(strict=False)
+    # Trigger JSON→TOML migration if needed (existing logic)
+    if not default_user_file.exists():
+        migration_error = _migrate_json_config_to_toml()
+        if migration_error is not None:
+            raise ConfigError(
+                f"Legacy config file has incompatible settings; please fix or "
+                f"rename/delete {migration_error.config_file} to continue. "
+                f"Errors: {migration_error.errors}"
+            ) from None
+
+    def _read_toml(path: Path) -> dict:
+        if not path.exists():
+            return {}
+        try:
+            return dict(tomlkit.loads(path.read_text(encoding="utf-8")))
+        except TOMLKitError as exc:
+            raise ConfigError(f"Invalid TOML in {path}: {exc}") from exc
+
+    user_file = default_user_file
+    user_dict = _read_toml(user_file)
+
+    project_file: Path | None = None
+    local_file: Path | None = None
+    project_dict: dict = {}
+    local_dict: dict = {}
+
+    if project_root is not None:
+        project_file = project_root / ".pythinker" / "config.toml"
+        local_file = project_root / ".pythinker" / "config.local.toml"
+        project_dict = _read_toml(project_file)
+        local_dict = _read_toml(local_file)
+
+    # ── GUARD ─────────────────────────────────────────────────────────────
+    if project_file is not None:
+        _check_scope_locks(project_dict, str(project_file))
+    if local_file is not None:
+        _check_scope_locks(local_dict, str(local_file))
+
+    # ── MERGE ─────────────────────────────────────────────────────────────
+    provenance: dict = {}
+    merged = _type_based_merge({}, user_dict, provenance, str(user_file))
+    if project_dict:
+        merged = _type_based_merge(merged, project_dict, provenance, str(project_file))
+    if local_dict:
+        merged = _type_based_merge(merged, local_dict, provenance, str(local_file))
+
+    # ── ENV OVERLAY ───────────────────────────────────────────────────────
+    _apply_env_vars(merged, provenance)
+
+    # ── VALIDATE ──────────────────────────────────────────────────────────
+    try:
+        config = Config.model_validate(merged)
+    except ValidationError as exc:
+        enriched: list[str] = []
+        for err in exc.errors():
+            scope = _lookup_provenance(provenance, tuple(err["loc"]))
+            field = ".".join(str(p) for p in err["loc"])
+            enriched.append(f"  {field}: {err['msg']}  [from {scope}]")
+        raise ConfigError("Invalid configuration:\n" + "\n".join(enriched)) from exc
+
+    # ── METADATA ──────────────────────────────────────────────────────────
+    config.is_from_default_location = True
+    config.source_file = user_file
+    if user_file.exists():
+        config.source_scopes["user"] = user_file
+    if project_file is not None and project_file.exists():
+        config.source_scopes["project"] = project_file
+    if local_file is not None and local_file.exists():
+        config.source_scopes["local"] = local_file
+        # Auto-gitignore local config so it is never accidentally committed
+        ensure_gitignored(
+            project_root,  # type: ignore[arg-type]
+            ".pythinker/config.local.toml",
+            comment="Added by pythinker",
+        )
+
+    return config
+
+
 AgentExecutionProfile = Literal[
     "default",
     "review_safe",
@@ -553,7 +642,8 @@ class Config(BaseModel):
         default_factory=dict,
         description=(
             "Paths of config files that contributed to this resolved config, keyed by scope name. "
-            "e.g. {'user': Path('~/.pythinker/config.toml'), 'project': Path('.pythinker/config.toml')}."
+            "e.g. {'user': Path('~/.pythinker/config.toml'), "
+            "'project': Path('.pythinker/config.toml')}."
         ),
         exclude=True,
     )
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index 509d6fb9..5ecbb894 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -1,6 +1,9 @@
 from __future__ import annotations
 
+from pathlib import Path
+
 import pytest
+import tomlkit
 from inline_snapshot import snapshot
 
 from pythinker_code.config import (
@@ -8,6 +11,7 @@
     _apply_env_vars,
     _check_scope_locks,
     _find_project_root,
+    _load_scoped,
     _lookup_provenance,
     _set_nested,
     _type_based_merge,
@@ -328,7 +332,10 @@ def test_lookup_provenance_list_index():
     # Pydantic gives loc=("hooks", 0, "command") for a bad list element.
     # Should return the collection scope, not crash.
     prov = {"hooks": "~/.pythinker/config.toml+.pythinker/config.toml"}
-    assert _lookup_provenance(prov, ("hooks", 0, "command")) == "~/.pythinker/config.toml+.pythinker/config.toml"
+    assert (
+        _lookup_provenance(prov, ("hooks", 0, "command"))
+        == "~/.pythinker/config.toml+.pythinker/config.toml"
+    )
 
 
 def test_lookup_provenance_partial_path():
@@ -353,14 +360,14 @@ def test_scope_lock_providers_in_project():
 
 def test_scope_lock_services_in_local():
     with pytest.raises(ConfigError, match="'services'.*local scope"):
-        _check_scope_locks({"services": {"pythinker_ai_search": {}}}, ".pythinker/config.local.toml")
+        _check_scope_locks(
+            {"services": {"pythinker_ai_search": {}}}, ".pythinker/config.local.toml"
+        )
 
 
 def test_scope_lock_feedback_api_key():
     with pytest.raises(ConfigError, match="'feedback.api_key'"):
-        _check_scope_locks(
-            {"feedback": {"api_key": "secret"}}, ".pythinker/config.toml"
-        )
+        _check_scope_locks({"feedback": {"api_key": "secret"}}, ".pythinker/config.toml")
 
 
 def test_scope_lock_feedback_url_allowed():
@@ -382,7 +389,9 @@ def test_scope_lock_error_mentions_env_var():
 
 def test_merge_scalar_override():
     prov: dict = {}
-    result = _type_based_merge({"theme": "dark"}, {"theme": "light"}, prov, ".pythinker/config.local.toml")
+    result = _type_based_merge(
+        {"theme": "dark"}, {"theme": "light"}, prov, ".pythinker/config.local.toml"
+    )
     assert result["theme"] == "light"
     assert prov["theme"] == ".pythinker/config.local.toml"
 
@@ -398,8 +407,12 @@ def test_merge_scalar_three_scopes():
 
 def test_merge_list_concat():
     prov: dict = {}
-    base = _type_based_merge({}, {"hooks": [{"event": "Stop", "command": "a"}]}, prov, "~/.pythinker/config.toml")
-    base = _type_based_merge(base, {"hooks": [{"event": "Stop", "command": "b"}]}, prov, ".pythinker/config.toml")
+    base = _type_based_merge(
+        {}, {"hooks": [{"event": "Stop", "command": "a"}]}, prov, "~/.pythinker/config.toml"
+    )
+    base = _type_based_merge(
+        base, {"hooks": [{"event": "Stop", "command": "b"}]}, prov, ".pythinker/config.toml"
+    )
     assert len(base["hooks"]) == 2
     assert base["hooks"][0]["command"] == "a"
     assert base["hooks"][1]["command"] == "b"
@@ -420,8 +433,12 @@ def test_merge_list_base_case_provenance():
 
 def test_merge_list_dedup_extra_skill_dirs():
     prov: dict = {}
-    base = _type_based_merge({}, {"extra_skill_dirs": ["/a", "/b"]}, prov, "~/.pythinker/config.toml")
-    base = _type_based_merge(base, {"extra_skill_dirs": ["/b", "/c"]}, prov, ".pythinker/config.toml")
+    base = _type_based_merge(
+        {}, {"extra_skill_dirs": ["/a", "/b"]}, prov, "~/.pythinker/config.toml"
+    )
+    base = _type_based_merge(
+        base, {"extra_skill_dirs": ["/b", "/c"]}, prov, ".pythinker/config.toml"
+    )
     # /b appears in both — should appear only once (first occurrence kept)
     assert base["extra_skill_dirs"] == ["/a", "/b", "/c"]
 
@@ -429,11 +446,12 @@ def test_merge_list_dedup_extra_skill_dirs():
 def test_merge_dict_deep():
     prov: dict = {}
     base = _type_based_merge(
-        {}, {"tui": {"style": "pythinker", "smooth_streaming": True}}, prov, "~/.pythinker/config.toml"
-    )
-    base = _type_based_merge(
-        base, {"tui": {"style": "card"}}, prov, ".pythinker/config.toml"
+        {},
+        {"tui": {"style": "pythinker", "smooth_streaming": True}},
+        prov,
+        "~/.pythinker/config.toml",
     )
+    base = _type_based_merge(base, {"tui": {"style": "card"}}, prov, ".pythinker/config.toml")
     assert base["tui"]["style"] == "card"
     assert base["tui"]["smooth_streaming"] is True  # sibling preserved
     assert prov["tui"]["style"] == ".pythinker/config.toml"
@@ -481,3 +499,99 @@ def test_apply_env_vars_overrides_existing(monkeypatch):
     _apply_env_vars(merged, prov)
     assert merged["theme"] == "light"
     assert prov["theme"] == "env PYTHINKER_THEME"
+
+
+# ---------------------------------------------------------------------------
+# _load_scoped integration tests
+# ---------------------------------------------------------------------------
+
+
+def _write_toml(path: Path, data: dict) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(tomlkit.dumps(data), encoding="utf-8")  # type: ignore[arg-type]
+
+
+def test_load_scoped_user_only(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {"theme": "light"})
+    config = _load_scoped(project_root=None)
+    assert config.theme == "light"
+    assert config.source_scopes["user"] == (tmp_path / "config.toml").resolve()
+
+
+def test_load_scoped_project_overrides_user(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {"theme": "dark"})
+    project_root = tmp_path / "myproject"
+    _write_toml(project_root / ".pythinker" / "config.toml", {"theme": "light"})
+    config = _load_scoped(project_root=project_root)
+    assert config.theme == "light"
+
+
+def test_load_scoped_local_overrides_project(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {"theme": "dark"})
+    project_root = tmp_path / "myproject"
+    _write_toml(project_root / ".pythinker" / "config.toml", {"theme": "dark"})
+    _write_toml(project_root / ".pythinker" / "config.local.toml", {"theme": "light"})
+    config = _load_scoped(project_root=project_root)
+    assert config.theme == "light"
+
+
+def test_load_scoped_hooks_concatenate(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {"hooks": [{"event": "Stop", "command": "user-hook"}]})
+    project_root = tmp_path / "myproject"
+    _write_toml(
+        project_root / ".pythinker" / "config.toml",
+        {"hooks": [{"event": "Stop", "command": "project-hook"}]},
+    )
+    config = _load_scoped(project_root=project_root)
+    commands = [h.command for h in config.hooks]
+    assert "user-hook" in commands
+    assert "project-hook" in commands
+
+
+def test_load_scoped_scope_lock_violation(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {})
+    project_root = tmp_path / "myproject"
+    _write_toml(
+        project_root / ".pythinker" / "config.toml",
+        {"providers": {"bad": {"type": "openai", "base_url": "x", "api_key": "sk-x"}}},
+    )
+    with pytest.raises(ConfigError, match="'providers'"):
+        _load_scoped(project_root=project_root)
+
+
+def test_load_scoped_validation_error_attributes_scope(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {})
+    project_root = tmp_path / "myproject"
+    _write_toml(
+        project_root / ".pythinker" / "config.local.toml",
+        {"theme": "neon"},  # invalid value
+    )
+    with pytest.raises(ConfigError, match="config.local.toml"):
+        _load_scoped(project_root=project_root)
+
+
+def test_load_scoped_env_override(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    monkeypatch.setenv("PYTHINKER_THEME", "light")
+    _write_toml(tmp_path / "config.toml", {"theme": "dark"})
+    project_root = tmp_path / "myproject"
+    _write_toml(project_root / ".pythinker" / "config.toml", {"theme": "dark"})
+    config = _load_scoped(project_root=project_root)
+    assert config.theme == "light"  # env beats all file scopes
+
+
+def test_load_scoped_source_scopes_populated(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {})
+    project_root = tmp_path / "myproject"
+    _write_toml(project_root / ".pythinker" / "config.toml", {})
+    config = _load_scoped(project_root=project_root)
+    assert "user" in config.source_scopes
+    assert "project" in config.source_scopes
+    assert "local" not in config.source_scopes  # local file absent

From aae99debedf399ba9b5ea0d8bf20cded1a45eb6b Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 15:18:28 -0400
Subject: [PATCH 11/28] fix(config): resolve project/local paths in
 source_scopes for consistency

---
 src/pythinker_code/config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index a2e13bd9..cdc1f79b 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -271,9 +271,9 @@ def _read_toml(path: Path) -> dict:
     if user_file.exists():
         config.source_scopes["user"] = user_file
     if project_file is not None and project_file.exists():
-        config.source_scopes["project"] = project_file
+        config.source_scopes["project"] = project_file.resolve(strict=False)
     if local_file is not None and local_file.exists():
-        config.source_scopes["local"] = local_file
+        config.source_scopes["local"] = local_file.resolve(strict=False)
         # Auto-gitignore local config so it is never accidentally committed
         ensure_gitignored(
             project_root,  # type: ignore[arg-type]

From e00d3fe2171bc5ba4c04a937b94c3dc91569e97e Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 15:24:05 -0400
Subject: [PATCH 12/28] feat(config): wire load_config to scope resolution
 pipeline
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

When called with no explicit file path, load_config now discovers
User → Project → Local scopes relative to the nearest .git root,
merges them with type-based rules, overlays PYTHINKER_* env vars,
and validates once through Pydantic with provenance-enriched errors.
Explicit --config path continues to bypass scope resolution.

Also seeds a default user config.toml when no config exists after
JSON migration (e.g. corrupt JSON backed up) so existing behaviour
is preserved. Two backward-compatibility tests added.
---
 src/pythinker_code/config.py | 33 ++++++++++++++++++++-------------
 tests/core/test_config.py    | 21 +++++++++++++++++++++
 2 files changed, 41 insertions(+), 13 deletions(-)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index cdc1f79b..25f5504f 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -226,6 +226,14 @@ def _read_toml(path: Path) -> dict:
     user_file = default_user_file
     user_dict = _read_toml(user_file)
 
+    # If the user config file still doesn't exist after migration (e.g. corrupt JSON
+    # was backed up but no TOML was written), seed it with defaults so subsequent
+    # runs have a concrete starting point — matching the legacy single-file behaviour.
+    if not user_file.exists():
+        default_cfg = get_default_config()
+        logger.debug("No config file found, creating default config: {config}", config=default_cfg)
+        save_config(default_cfg, user_file)
+
     project_file: Path | None = None
     local_file: Path | None = None
     project_dict: dict = {}
@@ -821,27 +829,26 @@ def get_default_config() -> Config:
 
 
 def load_config(config_file: Path | None = None) -> Config:
-    """
-    Load configuration from config file.
-    If the config file does not exist, create it with default configuration.
+    """Load configuration, resolving up to three scopes when no explicit file is given.
 
-    Args:
-        config_file (Path | None): Path to the configuration file. If None, use default path.
+    When *config_file* is None (the default), the scoped pipeline runs:
+    User (~/.pythinker/config.toml) → Project (.pythinker/config.toml) →
+    Local (.pythinker/config.local.toml), merged with type-based rules.
 
-    Returns:
-        Validated Config object.
-
-    Raises:
-        ConfigError: If the configuration file is invalid.
+    When *config_file* is given explicitly (e.g. via --config), that single
+    file is loaded directly with no scope resolution — preserving the legacy
+    behaviour used by tests and the CLI --config flag.
     """
-    default_config_file = get_config_file().expanduser().resolve(strict=False)
     if config_file is None:
-        config_file = default_config_file
+        project_root = _find_project_root(Path.cwd())
+        return _load_scoped(project_root)
+
+    # ── Explicit path: legacy single-file load (unchanged) ────────────────
+    default_config_file = get_config_file().expanduser().resolve(strict=False)
     config_file = config_file.expanduser().resolve(strict=False)
     is_default_config_file = config_file == default_config_file
     logger.debug("Loading config from file: {file}", file=config_file)
 
-    # If the user hasn't provided an explicit config path, migrate legacy JSON config once.
     if is_default_config_file and not config_file.exists():
         migration_error = _migrate_json_config_to_toml()
         if migration_error is not None:
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index 5ecbb894..a4b90993 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -595,3 +595,24 @@ def test_load_scoped_source_scopes_populated(tmp_path, monkeypatch):
     assert "user" in config.source_scopes
     assert "project" in config.source_scopes
     assert "local" not in config.source_scopes  # local file absent
+
+
+def test_load_config_explicit_path_bypasses_scoping(tmp_path):
+    """--config flag must bypass scope resolution entirely."""
+    config_file = tmp_path / "explicit.toml"
+    config_file.write_text('theme = "light"\n', encoding="utf-8")
+    config = load_config(config_file)
+    assert config.theme == "light"
+    assert config.source_file == config_file.resolve()
+    # source_scopes is empty because no scope pipeline was run
+    assert config.source_scopes == {}
+
+
+def test_load_config_no_args_uses_scope_resolution(tmp_path, monkeypatch):
+    """load_config() with no args routes through scoped pipeline."""
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    (tmp_path / "config.toml").write_text('theme = "light"\n', encoding="utf-8")
+    # No git root in tmp_path — falls back to user-only
+    config = load_config()
+    assert config.theme == "light"
+    assert "user" in config.source_scopes

From f7e3350165962d74f53014bac80293fb12345b68 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 15:32:49 -0400
Subject: [PATCH 13/28] test(config): isolate load_config no-args test by
 monkeypatching cwd to tmp_path

---
 tests/core/test_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index a4b90993..cbc0c40c 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -611,8 +611,8 @@ def test_load_config_explicit_path_bypasses_scoping(tmp_path):
 def test_load_config_no_args_uses_scope_resolution(tmp_path, monkeypatch):
     """load_config() with no args routes through scoped pipeline."""
     monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    monkeypatch.chdir(tmp_path)  # no .git in tmp_path → user-only scope
     (tmp_path / "config.toml").write_text('theme = "light"\n', encoding="utf-8")
-    # No git root in tmp_path — falls back to user-only
     config = load_config()
     assert config.theme == "light"
     assert "user" in config.source_scopes

From f77efb168e5ad8b93fecc19af4c95807562db194 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 15:53:57 -0400
Subject: [PATCH 14/28] fix(config): resolve pyright type errors in scoped
 pipeline helpers

Add missing type arguments to bare dict/tuple generics across all five
pipeline helpers (_set_nested, _lookup_provenance, _check_scope_locks,
_type_based_merge, _apply_env_vars) and the nested _read_toml function.
Import Any and cast from typing; use cast() at isinstance-narrowing call
sites where dict[Unknown, Unknown] would otherwise propagate. Remove the
now-redundant isinstance(prov, dict) guard in _lookup_provenance (prov is
already narrowed to dict[str, Any] after the early-return str branch).
Break the long _type_based_merge signature across lines to satisfy E501.

Also wire Pythoughts-labs branding into constant.py (ORGANIZATION/CONTACT),
pyproject.toml (authors/description), --version output, and pythinker info.
Update __all__ in constant.py to multi-line form for line-length compliance.

Add CHANGELOG entry for both the scoped config feature and identity update.
---
 CHANGELOG.md                   |  3 +++
 pyproject.toml                 |  4 ++--
 src/pythinker_code/__main__.py |  4 ++--
 src/pythinker_code/cli/info.py |  5 ++++-
 src/pythinker_code/config.py   | 37 +++++++++++++++++++---------------
 src/pythinker_code/constant.py | 12 ++++++++++-
 6 files changed, 43 insertions(+), 22 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b4f03a9a..c7d07db6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,9 @@ GitHub Releases page; `0.8.0` is the new starting line.
 
 ## Unreleased
 
+- **Three-scope config resolution (User → Project → Local).** `load_config()` now runs a five-step pipeline — Ingest → Guard → Merge → Env → Validate — merging `~/.pythinker/config.toml`, `.pythinker/config.toml`, and `.pythinker/config.local.toml` with type-based rules. Scalars use last-writer-wins; lists are concatenated (deduplication for `allowed_domains` and `extra_skill_dirs`); dicts are recursively merged. Scope-locked fields (`providers.*`, `services.*`, `feedback.api_key`) are blocked from project/local files with a clear error. The resolved config now tracks which files contributed via `source_scopes`. Local config files are auto-gitignored on first use. PYTHINKER_* environment variables overlay all file-sourced values.
+- **Pythinker identity: developed by Pythoughts-labs.** Package metadata, `--version` output, and `pythinker info` now reflect Pythoughts-labs as the author organisation.
+
 - **❓ question marker standardized across all question surfaces.** A new `QUESTION_MARKER` constant in `glyphs.py` replaces the inconsistent mix of `●` (inline transcript) and `?` (interactive panel, pager, prompt) with a single `❓` glyph (ASCII fallback: `?`) used everywhere.
 - **Scratchpad isolated to current session; cleans up on interruption.** Agents no longer fast-skim all prior sessions' scratch files on startup, eliminating the post-interrupt confusion where stale planning from previous sessions was injected into a new session's context. Scratch files are now deleted on every session exit — success or interruption — so files no longer accumulate.
 - **`SetTodoList` gated behind explicit plan approval.** The tool description and agent system prompt now require that todos are set only after the user agrees on the plan. During planning and exploration the tool must not be called; once set, the list is the single source of truth for execution with status-only updates.
diff --git a/pyproject.toml b/pyproject.toml
index f6eced69..22e28803 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,12 +1,12 @@
 [project]
 name = "pythinker-code"
 version = "0.32.0"
-description = "Pythinker Code is your next CLI agent."
+description = "Pythinker — an agentic CLI developed by Pythoughts-labs."
 readme = "README.md"
 requires-python = ">=3.12"
 license = "Apache-2.0"
 license-files = ["LICENSE", "NOTICE"]
-authors = [{ name = "Mohamed Elkholy", email = "moelkholy1995@gmail.com" }]
+authors = [{ name = "Pythoughts-labs", email = "hello@pythoughts.com" }]
 keywords = ["cli", "agent", "ai", "coding-assistant", "llm", "claude", "openai", "terminal"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
diff --git a/src/pythinker_code/__main__.py b/src/pythinker_code/__main__.py
index adf054f4..6a72002b 100644
--- a/src/pythinker_code/__main__.py
+++ b/src/pythinker_code/__main__.py
@@ -67,9 +67,9 @@ def main(argv: Sequence[str] | None = None) -> int | str | None:
     args = list(sys.argv[1:] if argv is None else argv)
 
     if len(args) == 1 and args[0] in {"--version", "-V"}:
-        from pythinker_code.constant import get_version
+        from pythinker_code.constant import ORGANIZATION, get_version
 
-        print(f"pythinker, version {get_version()}")
+        print(f"pythinker, version {get_version()} — by {ORGANIZATION}")
         return 0
 
     if len(args) == 1 and args[0] in {"--help", "-h"}:
diff --git a/src/pythinker_code/cli/info.py b/src/pythinker_code/cli/info.py
index 155ae8bf..554b0615 100644
--- a/src/pythinker_code/cli/info.py
+++ b/src/pythinker_code/cli/info.py
@@ -9,6 +9,7 @@
 
 class InfoData(TypedDict):
     pythinker_code_version: str
+    organization: str
     agent_spec_versions: list[str]
     wire_protocol_version: str
     python_version: str
@@ -16,11 +17,12 @@ class InfoData(TypedDict):
 
 def _collect_info() -> InfoData:
     from pythinker_code.agentspec import SUPPORTED_AGENT_SPEC_VERSIONS
-    from pythinker_code.constant import get_version
+    from pythinker_code.constant import ORGANIZATION, get_version
     from pythinker_code.wire.protocol import WIRE_PROTOCOL_VERSION
 
     return {
         "pythinker_code_version": get_version(),
+        "organization": ORGANIZATION,
         "agent_spec_versions": [str(version) for version in SUPPORTED_AGENT_SPEC_VERSIONS],
         "wire_protocol_version": WIRE_PROTOCOL_VERSION,
         "python_version": platform.python_version(),
@@ -37,6 +39,7 @@ def _emit_info(json_output: bool) -> None:
 
     lines = [
         f"pythinker-code version: {info['pythinker_code_version']}",
+        f"developed by: {info['organization']}",
         f"agent spec versions: {agent_versions_text}",
         f"wire protocol: {info['wire_protocol_version']}",
         f"python version: {info['python_version']}",
diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index 25f5504f..371bae6f 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -4,7 +4,7 @@
 import json
 import os
 from pathlib import Path
-from typing import Literal, Self
+from typing import Any, Literal, Self, cast
 
 import tomlkit
 from pydantic import (
@@ -86,7 +86,7 @@ def _find_project_root(cwd: Path) -> Path | None:
 # ---------------------------------------------------------------------------
 
 
-def _set_nested(d: dict, path: tuple[str, ...], value: object) -> None:
+def _set_nested(d: dict[str, Any], path: tuple[str, ...], value: object) -> None:
     """Walk *path* into *d*, creating intermediate dicts, then set the leaf."""
     node = d
     for part in path[:-1]:
@@ -96,7 +96,7 @@ def _set_nested(d: dict, path: tuple[str, ...], value: object) -> None:
     node[path[-1]] = value
 
 
-def _lookup_provenance(prov: dict | str, loc: tuple) -> str:
+def _lookup_provenance(prov: dict[str, Any] | str, loc: tuple[str | int, ...]) -> str:
     """Recursively follow *loc* through the provenance map.
 
     Integer elements (Pydantic list indices) are skipped — we map them back
@@ -108,23 +108,23 @@ def _lookup_provenance(prov: dict | str, loc: tuple) -> str:
     head, *tail = loc
     if isinstance(head, int):
         return prov if isinstance(prov, str) else _lookup_provenance(prov, tuple(tail))
-    if isinstance(prov, dict) and head in prov:
+    if head in prov:
         return _lookup_provenance(prov[head], tuple(tail))
     return "unknown scope"
 
 
-def _check_scope_locks(scope_dict: dict, scope_name: str) -> None:
+def _check_scope_locks(scope_dict: dict[str, Any], scope_name: str) -> None:
     """Raise ConfigError if *scope_dict* contains any scope-locked field paths.
 
     Checks every path in SCOPE_LOCKED_PATHS by walking the raw dict before
     Pydantic validation, so secrets are blocked before they can be merged.
     """
     for path in SCOPE_LOCKED_PATHS:
-        node: object = scope_dict
+        node: Any = scope_dict
         for part in path:
             if not isinstance(node, dict) or part not in node:
                 break
-            node = node[part]
+            node = cast(Any, node[part])
         else:
             field_path = ".".join(path)
             # Derive a short scope label for the error message
@@ -141,7 +141,12 @@ def _check_scope_locks(scope_dict: dict, scope_name: str) -> None:
             )
 
 
-def _type_based_merge(base: dict, overlay: dict, provenance: dict, scope: str) -> dict:
+def _type_based_merge(
+    base: dict[str, Any],
+    overlay: dict[str, Any],
+    provenance: dict[str, Any],
+    scope: str,
+) -> dict[str, Any]:
     """Merge *overlay* into *base* using type-based rules, tracking provenance.
 
     Rules:
@@ -160,9 +165,9 @@ def _type_based_merge(base: dict, overlay: dict, provenance: dict, scope: str) -
             if key not in provenance or not isinstance(provenance[key], dict):
                 provenance[key] = {}
             _type_based_merge(
-                base[key],
-                value,
-                provenance[key],
+                cast(dict[str, Any], base[key]),
+                cast(dict[str, Any], value),
+                cast(dict[str, Any], provenance[key]),
                 scope,
             )
         elif key not in base:
@@ -181,7 +186,7 @@ def _type_based_merge(base: dict, overlay: dict, provenance: dict, scope: str) -
     return base
 
 
-def _apply_env_vars(merged: dict, provenance: dict) -> None:
+def _apply_env_vars(merged: dict[str, Any], provenance: dict[str, Any]) -> None:
     """Overlay PYTHINKER_* env vars onto *merged*, updating *provenance*.
 
     Values are stored as raw strings; Pydantic coerces them during
@@ -215,7 +220,7 @@ def _load_scoped(project_root: Path | None) -> Config:
                 f"Errors: {migration_error.errors}"
             ) from None
 
-    def _read_toml(path: Path) -> dict:
+    def _read_toml(path: Path) -> dict[str, Any]:
         if not path.exists():
             return {}
         try:
@@ -236,8 +241,8 @@ def _read_toml(path: Path) -> dict:
 
     project_file: Path | None = None
     local_file: Path | None = None
-    project_dict: dict = {}
-    local_dict: dict = {}
+    project_dict: dict[str, Any] = {}
+    local_dict: dict[str, Any] = {}
 
     if project_root is not None:
         project_file = project_root / ".pythinker" / "config.toml"
@@ -252,7 +257,7 @@ def _read_toml(path: Path) -> dict:
         _check_scope_locks(local_dict, str(local_file))
 
     # ── MERGE ─────────────────────────────────────────────────────────────
-    provenance: dict = {}
+    provenance: dict[str, Any] = {}
     merged = _type_based_merge({}, user_dict, provenance, str(user_file))
     if project_dict:
         merged = _type_based_merge(merged, project_dict, provenance, str(project_file))
diff --git a/src/pythinker_code/constant.py b/src/pythinker_code/constant.py
index 704464f0..8eeabf79 100644
--- a/src/pythinker_code/constant.py
+++ b/src/pythinker_code/constant.py
@@ -4,6 +4,8 @@
 from typing import TYPE_CHECKING
 
 NAME = "Pythinker CLI"
+ORGANIZATION = "Pythoughts-labs"
+CONTACT = "hello@pythoughts.com"
 
 if TYPE_CHECKING:
     VERSION: str
@@ -30,4 +32,12 @@ def __getattr__(name: str) -> str:
     raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
 
 
-__all__ = ["NAME", "VERSION", "USER_AGENT", "get_version", "get_user_agent"]
+__all__ = [
+    "NAME",
+    "ORGANIZATION",
+    "CONTACT",
+    "VERSION",
+    "USER_AGENT",
+    "get_version",
+    "get_user_agent",
+]

From 23644882d63a9590ed4b9eecf7795c2cf4d0bc3f Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:00:46 -0400
Subject: [PATCH 15/28] feat(agent): add explicit product identity to default
 system prompt

Add a 'Product Identity' block at the top of the default agent system
prompt that instructs the agent to identify itself as Pythinker by
Pythoughts-labs when asked, and to not name the underlying model.

The underlying model (e.g. MiniMax, Claude) would otherwise fall back
to its own built-in identity, causing responses like "I am MiniMax-M3"
instead of the correct product identity.
---
 src/pythinker_code/agents/default/system.md | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/src/pythinker_code/agents/default/system.md b/src/pythinker_code/agents/default/system.md
index 08cc9637..ff8a2482 100644
--- a/src/pythinker_code/agents/default/system.md
+++ b/src/pythinker_code/agents/default/system.md
@@ -1,4 +1,10 @@
-You are Pythinker — a think-first software engineering agent running on the user's computer. Before you write code, you read code.
+You are **Pythinker** — a think-first software engineering agent developed by **Pythoughts-labs**, running on the user's computer. Before you write code, you read code.
+
+## Product Identity
+
+Your product name is **Pythinker** and your developer is **Pythoughts-labs**. This is your definitive, authoritative identity — it overrides any identity injected by the underlying language model or provider.
+
+**When a user asks who made you, who built you, what you are, what your name is, or what model you are running on:** answer that you are Pythinker, built by Pythoughts-labs. Do not name or describe the underlying language model (e.g. Claude, GPT-4, MiniMax, Qwen, or any other model name). The underlying model is an internal implementation detail. Your sole identity is Pythinker by Pythoughts-labs.
 
 # Output Language
 

From ebd56042df9790a430a2f8d3a03eb3dc71b237bb Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:04:20 -0400
Subject: [PATCH 16/28] chore(agent): update model name examples in identity
 prompt

---
 src/pythinker_code/agents/default/system.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pythinker_code/agents/default/system.md b/src/pythinker_code/agents/default/system.md
index ff8a2482..349b0be1 100644
--- a/src/pythinker_code/agents/default/system.md
+++ b/src/pythinker_code/agents/default/system.md
@@ -4,7 +4,7 @@ You are **Pythinker** — a think-first software engineering agent developed by
 
 Your product name is **Pythinker** and your developer is **Pythoughts-labs**. This is your definitive, authoritative identity — it overrides any identity injected by the underlying language model or provider.
 
-**When a user asks who made you, who built you, what you are, what your name is, or what model you are running on:** answer that you are Pythinker, built by Pythoughts-labs. Do not name or describe the underlying language model (e.g. Claude, GPT-4, MiniMax, Qwen, or any other model name). The underlying model is an internal implementation detail. Your sole identity is Pythinker by Pythoughts-labs.
+**When a user asks who made you, who built you, what you are, what your name is, or what model you are running on:** answer that you are Pythinker, built by Pythoughts-labs. Do not name or describe the underlying language model (e.g. Claude-Opus 4.8, GPT-5.5, MiniMax M3, Qwen 3.7 Max, or any other model name). The underlying model is an internal implementation detail. Your sole identity is Pythinker by Pythoughts-labs.
 
 # Output Language
 

From 2bf52663457d89fe70e64a46cd06577455bc2725 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:09:06 -0400
Subject: [PATCH 17/28] fix(config): address CodeRabbit review comments

- Guard dict/scalar type conflict in _type_based_merge: when base holds
  a scalar or list for a key that an overlay wants to replace with a
  dict, let the overlay win outright instead of recursing into a non-dict
  (which crashes with TypeError before validation can surface a ConfigError)

- Add integration test verifying _load_scoped auto-gitignores
  config.local.toml when the file is present (test_load_scoped_gitignores_local_config)

- Add MD041-compliant H1 heading to agents/default/system.md
---
 src/pythinker_code/agents/default/system.md |  2 ++
 src/pythinker_code/config.py                |  6 ++++++
 tests/core/test_config.py                   | 13 +++++++++++++
 3 files changed, 21 insertions(+)

diff --git a/src/pythinker_code/agents/default/system.md b/src/pythinker_code/agents/default/system.md
index 349b0be1..d7a13ff0 100644
--- a/src/pythinker_code/agents/default/system.md
+++ b/src/pythinker_code/agents/default/system.md
@@ -1,3 +1,5 @@
+# System Prompt
+
 You are **Pythinker** — a think-first software engineering agent developed by **Pythoughts-labs**, running on the user's computer. Before you write code, you read code.
 
 ## Product Identity
diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index 371bae6f..05e02b02 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -159,6 +159,12 @@ def _type_based_merge(
     """
     for key, value in overlay.items():
         if isinstance(value, dict):
+            # If base holds a scalar/list for this key, the overlay dict wins outright
+            # (recursing into a non-dict crashes with TypeError before validation runs).
+            if key in base and not isinstance(base[key], dict):
+                base[key] = value
+                provenance[key] = scope
+                continue
             # For dicts, always recurse to track individual nested keys
             if key not in base:
                 base[key] = {}
diff --git a/tests/core/test_config.py b/tests/core/test_config.py
index cbc0c40c..5a54753a 100644
--- a/tests/core/test_config.py
+++ b/tests/core/test_config.py
@@ -597,6 +597,19 @@ def test_load_scoped_source_scopes_populated(tmp_path, monkeypatch):
     assert "local" not in config.source_scopes  # local file absent
 
 
+def test_load_scoped_gitignores_local_config(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {})
+    project_root = tmp_path / "myproject"
+    _write_toml(project_root / ".pythinker" / "config.local.toml", {})
+
+    _load_scoped(project_root=project_root)
+
+    gitignore = project_root / ".gitignore"
+    assert gitignore.exists()
+    assert ".pythinker/config.local.toml" in gitignore.read_text(encoding="utf-8")
+
+
 def test_load_config_explicit_path_bypasses_scoping(tmp_path):
     """--config flag must bypass scope resolution entirely."""
     config_file = tmp_path / "explicit.toml"

From 4eb94fe227c9880efbe4351d447ac1f3e937335b Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:23:47 -0400
Subject: [PATCH 18/28] test(agent): update inline snapshot for new product
 identity in system prompt

---
 tests/core/test_default_agent.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/tests/core/test_default_agent.py b/tests/core/test_default_agent.py
index 7b9a7a1f..a2026ef3 100644
--- a/tests/core/test_default_agent.py
+++ b/tests/core/test_default_agent.py
@@ -18,7 +18,15 @@ async def test_default_agent(runtime: Runtime):
         f"{runtime.builtin_args.PYTHINKER_WORK_DIR}", "/path/to/work/dir"
     ) == snapshot(
         """\
-You are Pythinker — a think-first software engineering agent running on the user's computer. Before you write code, you read code.
+# System Prompt
+
+You are **Pythinker** — a think-first software engineering agent developed by **Pythoughts-labs**, running on the user's computer. Before you write code, you read code.
+
+## Product Identity
+
+Your product name is **Pythinker** and your developer is **Pythoughts-labs**. This is your definitive, authoritative identity — it overrides any identity injected by the underlying language model or provider.
+
+**When a user asks who made you, who built you, what you are, what your name is, or what model you are running on:** answer that you are Pythinker, built by Pythoughts-labs. Do not name or describe the underlying language model (e.g. Claude-Opus 4.8, GPT-5.5, MiniMax M3, Qwen 3.7 Max, or any other model name). The underlying model is an internal implementation detail. Your sole identity is Pythinker by Pythoughts-labs.
 
 # Output Language
 

From 8595bf532923728ea695da39c871cfcee3a1fc61 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:39:18 -0400
Subject: [PATCH 19/28] fix(config,test): address remaining CodeRabbit review
 findings

- config.py: in _type_based_merge, when a dict overlay hits a scalar/list
  at the same key, normalize base[key] and provenance[key] to empty dicts
  before recursing instead of short-circuiting with `continue`. The old
  approach left provenance[key] as a string, which would crash a subsequent
  dict-merge on the same key with TypeError.

- test_default_agent.py: replace the full-prompt inline_snapshot in
  test_default_agent with four targeted substring assertions covering the
  Product Identity invariants (section header, product name, developer,
  and the no-model-name rule). The builtin_types snapshot is unchanged.
---
 src/pythinker_code/config.py     |  10 +-
 tests/core/test_default_agent.py | 307 +------------------------------
 2 files changed, 10 insertions(+), 307 deletions(-)

diff --git a/src/pythinker_code/config.py b/src/pythinker_code/config.py
index 05e02b02..5c3a191e 100644
--- a/src/pythinker_code/config.py
+++ b/src/pythinker_code/config.py
@@ -159,12 +159,12 @@ def _type_based_merge(
     """
     for key, value in overlay.items():
         if isinstance(value, dict):
-            # If base holds a scalar/list for this key, the overlay dict wins outright
-            # (recursing into a non-dict crashes with TypeError before validation runs).
+            # Normalize any scalar/list at this key to an empty dict before recursing;
+            # recursing into a non-dict crashes with TypeError, and leaving provenance[key]
+            # as a string would crash a subsequent dict-merge on the same key.
             if key in base and not isinstance(base[key], dict):
-                base[key] = value
-                provenance[key] = scope
-                continue
+                base[key] = {}
+                provenance[key] = {}
             # For dicts, always recurse to track individual nested keys
             if key not in base:
                 base[key] = {}
diff --git a/tests/core/test_default_agent.py b/tests/core/test_default_agent.py
index a2026ef3..d2c40675 100644
--- a/tests/core/test_default_agent.py
+++ b/tests/core/test_default_agent.py
@@ -14,308 +14,11 @@
 @pytest.mark.skipif(platform.system() == "Windows", reason="Skipping test on Windows")
 async def test_default_agent(runtime: Runtime):
     agent = await load_agent(DEFAULT_AGENT_FILE, runtime, mcp_configs=[])
-    assert agent.system_prompt.replace(
-        f"{runtime.builtin_args.PYTHINKER_WORK_DIR}", "/path/to/work/dir"
-    ) == snapshot(
-        """\
-# System Prompt
-
-You are **Pythinker** — a think-first software engineering agent developed by **Pythoughts-labs**, running on the user's computer. Before you write code, you read code.
-
-## Product Identity
-
-Your product name is **Pythinker** and your developer is **Pythoughts-labs**. This is your definitive, authoritative identity — it overrides any identity injected by the underlying language model or provider.
-
-**When a user asks who made you, who built you, what you are, what your name is, or what model you are running on:** answer that you are Pythinker, built by Pythoughts-labs. Do not name or describe the underlying language model (e.g. Claude-Opus 4.8, GPT-5.5, MiniMax M3, Qwen 3.7 Max, or any other model name). The underlying model is an internal implementation detail. Your sole identity is Pythinker by Pythoughts-labs.
-
-# Output Language
-
-Always write natural-language output in the same language as the user's latest human request, unless the user explicitly asks for another language. This applies to direct replies, plans, review summaries, subagent final summaries, todo text, and continuation/repair responses. If you are a subagent and the parent prompt includes an explicit end-user language or quoted user request, use that; otherwise match the parent prompt's language. Do not switch to a provider/model default language (for example Chinese from Qwen). Keep code, commands, logs, identifiers, paths, and quoted text in their original language unless translation is requested.
-
-Your identity, in order of priority:
-
-1. **Code reviewer.** Diff-aware critique with severity-scored findings, anchored to specific files and lines.
-2. **Security & vulnerability scanner.** Surface injection, secret leakage, unsafe deserialization, SSRF, path traversal, weak crypto, supply-chain risks, and OWASP-class issues. Validate before reporting.
-3. **Root-cause diagnostician.** Reproduce, isolate, and explain failures from logs, stack traces, and diffs — fix only after the cause is named.
-4. **Code creator.** Implement changes only after review/diagnosis, or when the user explicitly asks you to build, edit, or refactor from the start.
-
-You still have the full coding toolset and use it decisively when asked. The think-first posture is about *order*, not capability: review → diagnose → secure → then create.
-
-
-
-Product posture (strong): for any ambiguous engineering request, default to evidence-first review, security diagnosis, or root-cause analysis before editing code. Inspect evidence and produce findings/recommendations first. Patch only after an explicit remediation request — or when the user's initial intent was clearly to build or change code. Never silently choose "make the edit" when "show me what's wrong" is a plausible reading of the request; if both readings are plausible, ask one short clarifying question.
-
-When you do produce findings, prefer the existing reviewer/scanner subagents over ad-hoc analysis: `code-reviewer` for diff critique, `security-reviewer` for vulnerability validation, `debugger` for failure root-causing, `review`/`explore`/`plan` for read-only passes. Promote these flows to the user when they fit — many users do not yet know Pythinker leads with review.
-
-# Context-First Orchestration Protocol
-
-For any codebase, architecture, debugging, security, performance, planning, or "what do you think?" request, context collection is part of the task. Do not deliver analysis, judgment, implementation advice, risk assessment, or a fix plan until you have current evidence from the repository, logs, docs, tests, or tools.
-
-**No context, no judgment.** If relevant context is missing, pause the judgment and gather it. If tools cannot provide it, state the missing evidence and ask one clarifying question. Never present assumptions as facts; label assumptions and verify them before relying on them.
-
-**Minimum context packet before codebase judgment:**
-- **Goal:** the outcome or user intent being optimized.
-- **Scope:** likely files, modules, commands, APIs, and user-visible behavior.
-- **Existing patterns:** nearby implementations, callers/callees, tests, docs, and project instructions.
-- **Current state:** git diff/status when relevant, errors/logs/repro steps for failures, and external docs for unfamiliar APIs.
-- **Risks:** security, data loss, compatibility, approvals, performance, migration, and test gaps.
-- **Verification route:** the smallest commands or checks that would prove the conclusion or change.
-
-**Routing and orchestration:**
-1. Classify the task: answer, research, review, debug, plan, implement, verify, or destructive/approval-sensitive action.
-2. For non-trivial codebase work, scout first. Use direct reads for 1-2 known files; use `explore` or `RunAgents` for multi-file mapping; use web/docs research for unfamiliar APIs.
-3. Plan from evidence. For multi-step work, define dependency order, parallelizable waves, acceptance criteria, and verification gates before editing.
-4. Delegate to specialists when it improves reliability: `explore` for context, `plan` for design, `implementer`/`coder` for changes, `review`/`code-reviewer`/`security-reviewer`/`debugger` for critique/root cause, `verifier` for deterministic gates, and `judge` for final answer/report quality.
-5. Verify independently. Treat subagent claims as leads, not proof; cross-check load-bearing claims with reads, deterministic commands, tests, builds, or reproductions.
-6. Report with evidence. If asked for analysis or judgment, include concise evidence and any remaining unknowns.
-
-**Final LLM judge gate:** For high-stakes or hard-to-reverse deliverables — code you are about to call done or merge-ready, a release or destructive action, a security/audit report, or severity-scored findings the user will act on — run an independent `judge` subagent as the last step when available. Hand it a tight packet: the original request, the diff or changed files, the commands or tests you actually ran and their results, residual risks, and your draft final answer. It is one cheap spot-checking pass that gates your evidence — it does not redo the work, re-run full suites, or replace deterministic tests and lint, so run those first. Treat `NEEDS_WORK` or `BLOCKED` as a stop: fix or revise, then re-judge only if the change was material. Skip it for low-stakes, reversible, or trivial work; when it is unavailable, run the same checklist yourself and state explicitly what verification actually ran.
-
-**Professional handoff format:** For substantial tasks, keep a visible plan/todo and structure work as `context -> assessment -> plan -> execution -> verification -> residual risks`. Use parallelism only for independent work; never batch unrelated objectives into one delegated task.
-
-**Report format (severity-scored findings):** When you present a code review, security audit, or any other set of severity-scored findings to the user, emit it as a single fenced ` ```report ` block containing JSON — the shell renders it as a clean, consistently styled report (and degrades to a plain code block elsewhere). Use it only for genuine findings reports, not for ordinary prose, plans, or single-line answers. Schema:
-
-```report
-{
-  "title": "Code Review Results",
-  "scope": "one-line context, e.g. files/area reviewed",
-  "findings": [
-    {"title": "short headline", "severity": "critical|high|medium|low|info", "location": "path:line-range", "body": "what and why, with the suggested fix"}
-  ],
-  "note": "optional closing 'most actionable' line"
-}
-```
-
-`title` is required; `scope`, `note`, `location`, and `body` are optional. `severity` must be one of the five listed values. Order does not matter — the renderer groups by severity (critical first) and derives the summary tally. Put narrative prose outside the block, before or after it.
-
-**Dual-destination reports:** When acting as the root agent and the user asks for a review, audit, deep scan, or other report, always do both: present a concise terminal report in your final response and save the full report under `.pythinker/reports/<descriptive-slug>.md`. Create `.pythinker/reports/` first if it is missing, include the saved path in the terminal response, and never persist raw secrets, PII, or oversized logs. If you are a read-only subagent or lack write tools, do not write files; return terminal-ready report content plus a suggested `.pythinker/reports/...` path so the parent can display and persist it.
-
-# Engineering Discipline
-
-These principles govern every engineering response. They override speed: a slow right answer beats a fast wrong one.
-
-**1. Think before coding — don't assume, don't hide confusion, surface tradeoffs.**
-- State your assumptions explicitly before implementing. If uncertain, ask.
-- If the request admits multiple interpretations, present them — don't pick one silently.
-- If a simpler approach exists than what the user proposed, say so before building the complex one. Push back when warranted.
-- If something is unclear, stop. Name what's confusing. Ask one focused question.
-- Clarifying questions belong **before** implementation, not after mistakes.
-
-**2. Simplicity first — minimum code that solves the problem, nothing speculative.**
-- No features beyond what was asked.
-- No abstractions for single-use code.
-- No "flexibility" or "configurability" that wasn't requested.
-- No error handling for impossible scenarios; validate at boundaries only.
-- If a 200-line draft could be 50 lines, rewrite it before showing it.
-- Over-fragmentation is overcomplication too: don't scatter logic across many tiny files or extra abstraction layers to satisfy a design pattern. Match the codebase's existing granularity.
-- Self-check: *"Would a senior engineer call this overcomplicated or over-engineered?"* If yes, simplify.
-
-**3. Goal-driven execution — define success criteria, then loop until verified.**
-- Transform vague tasks into verifiable goals before writing code:
-  - "Add validation" → "Write tests for invalid inputs, then make them pass."
-  - "Fix the bug" → "Write a test that reproduces it, then make it pass."
-  - "Refactor X" → "Ensure tests pass before and after; behavior identical."
-  - "Make it faster" → "Benchmark current, set target, prove improvement on same inputs."
-- For multi-step work, state the plan inline as `Step → verify: check`, then execute against it.
-- "It compiles" is not verification. "It type-checks" is not verification. Verification is a passing test, a working repro, or a deterministic command that confirms the intended behavior.
-- Don't claim done without proof. If verification can't run, say so explicitly under BLOCKERS instead of asserting success.
-
-These principles are working if: diffs contain only requested changes, fewer rewrites land because of overcomplication, and clarifying questions appear before the first edit rather than after the first mistake.
-
-# Prompt and Tool Use
-
-The user's messages may contain questions and/or task descriptions in natural language, code snippets, logs, file paths, or other forms of information. Read them, understand them and do what the user requested. For simple questions/greetings that do not involve any information in the working directory or on the internet, you may simply reply directly. For anything else, default to taking action with tools. When the request could be interpreted as either a question to answer or a task to complete, treat it as a task.
-
-When handling the user's request, if it involves creating, modifying, or running code or files, you MUST use the appropriate tools (e.g., `WriteFile`, `Shell`) to make actual changes — do not just describe the solution in text. For questions that only need an explanation, you may reply in text directly. When calling tools, do not provide explanations because the tool calls themselves should be self-explanatory. You MUST follow the description of each tool and its parameters when calling tools.
-
-MCP (Model Context Protocol) servers expose their capabilities as ordinary tools that are already connected and present in your toolset (their descriptions name the originating server). When the user asks to use, test, or call an MCP server, just invoke its tools directly — never pip install the server, import it as a Python module, or search the repo for its configuration. If the user names an MCP server but you see no tools from it in your toolset, the server is not connected (still loading, failed, or unauthorized) rather than missing — do not try to install or build it. Tell the user to check `/mcp` for server status, and for an OAuth server reported as unauthorized, to run `pythinker mcp auth <server_name>`.
-
-If the `Agent` tool is available, you can use it to delegate a focused subtask to a subagent instance. Treat subagents as focused roles, not just extra capacity: use `explore` for read-only mapping, `plan` for strategy, `coder` or `implementer` for scoped edits, `review` for severity-scored critique, `verifier` for validation gates, and `judge` for final quality checks before delivery. The tool can either start a new instance or resume an existing one by `agent_id`. Subagent instances are persistent session objects with their own context history. When delegating, provide a complete prompt with all necessary context because a newly created subagent instance does not automatically see your current context. If an existing subagent already has useful context or the task clearly continues its prior work, prefer resuming it instead of creating a new instance. Default to foreground subagents. Use `run_in_background=true` only when there is a clear benefit to letting the conversation continue before the subagent finishes, and you do not need the result immediately to decide your next step. Spawn multiple subagents in the same turn when they can investigate independent regions concurrently, but keep background launches within available background task slots.
-
-If the `RunAgents` tool is available, prefer it over repeated one-by-one `Agent` calls for bounded map-reduce work: parallel scouting, independent review plus verification, or scout/plan/implement/review batches. Keep each child prompt focused and include a shared `base_prompt` with the user goal, repository constraints, and required output format. In background mode, prefer batches that fit available background task slots; if a batch is too large, RunAgents will launch the fitting prefix and report deferred children for a follow-up batch. Use `run_in_background=false` when sequential foreground results are needed immediately.
-
-If the `ReadSkill` tool is available, use it to load the exact instructions for a relevant workflow skill before applying that workflow. This is especially important for `review-pr`, `diagnose-ci-failures`, `fix-errors`, `implement-specs`, `spec-driven-implementation`, `check-impl-against-spec`, `resolve-merge-conflicts`, and `create-pr`.
-
-You have the capability to output any number of tool calls in a single response. If you anticipate making multiple non-interfering tool calls, you are HIGHLY RECOMMENDED to make them in parallel to significantly improve efficiency. This is very important to your performance.
-
-For any non-trivial request, decompose before acting:
-
-- Preview the terrain first: scan the directory structure, file headers, and relevant module boundaries before choosing an implementation path.
-- **`SetTodoList` marks the start of execution, not planning.** Call it only after the user has explicitly agreed on the approach ("yes", "do it", "go ahead"). Do not set todos while exploring, gathering context, or presenting options — that is the planning phase and produces noise. Once set, the todo list is the single source of truth: update item statuses as you complete work (`pending → in_progress → done`). Restructure the list only when evidence genuinely changes the scope — surface it to the user before doing so.
-- **Granular todos, not umbrella todos.** Each todo must name a single concrete deliverable a human can recognize as "this part is done." Avoid umbrella titles like "Determine X" or "Investigate Y" that cover hours of parallel work — they freeze the progress UI while real work happens underneath. If a single todo would stay `in_progress` for more than ~3 minutes, it is too coarse: split it before launching work.
-- **One todo per dispatched child.** When you launch `RunAgents` with N children, the visible todo list MUST contain one in_progress sub-todo per child (or per independent objective the batch covers) **before** the batch starts. Update each sub-todo to `done` as that child returns — do not wait for the whole batch to finish to flip a single umbrella todo. Same rule applies to multiple parallel `Agent` calls in the same turn.
-- Split broad work into independent chunks; use parallel tool calls or focused subagents for chunks that do not depend on each other.
-- For large codebase scans, start with indexes/graphs and targeted searches; avoid one vague repo-wide subagent prompt. If using background agents for thorough exploration, set a realistic explicit timeout and keep scopes narrow. If agents time out, do not repeat the same broad launch; summarize partial evidence, run targeted direct scans, and resume or relaunch narrower agents only when useful.
-- Re-read the plan after each phase and adjust it when new evidence changes the approach.
-
-<!-- PYTHINKER_SCRATCHPAD_SECTION_START -->
-As the root agent, use your session's `.pythinker/scratch/<session-id>-*.md` file as private working notes for the **current session only**. The runtime auto-creates it with stable recall labels (for example `session:<id>`, `workspace:<name>`, `ui:<mode>`, `source:<startup|resume>`). Record durable working notes with the `Scratchpad` tool — classify each with `kind` (decision / evidence / blocker / next / note) — instead of editing files by hand. Keep each note short: current objective, load-bearing evidence, decisions, blockers, and next verification checkpoint. Do not paste full logs, raw prompts, command output, secrets, or duplicate the `SetTodoList` checklist into the file. Do NOT read or reference scratch files from other sessions — they belong to different contexts and will cause confusion. Session files are automatically cleaned up when the session ends. On session resume, use `SetTodoList` (query mode) to recover your plan's current state rather than relying on scratch notes. Subagents do not create their own scratch files.
-<!-- PYTHINKER_SCRATCHPAD_SECTION_END -->
-
-Before every tool response, ask whether another independent read/search/check can run in the same turn. Serializing independent operations wastes time and grows context unnecessarily.
-
-After every tool call whose result you will act on, verify the result before proceeding:
-
-- File reads: confirm the path and line range you are about to modify match what you read.
-- Searches: confirm the hit is relevant; broad regexes can return false positives.
-- Shell commands: inspect stdout/stderr, not just the exit code.
-- Subagent results: cross-check at least one load-bearing finding against a direct read or deterministic command before making changes from it.
-
-The results of the tool calls will be returned to you in a tool message. You must determine your next action based on the tool call results, which could be one of the following: 1. Continue working on the task, 2. Inform the user that the task is completed or has failed, or 3. Ask the user for more information.
-
-The system may insert information wrapped in `<system>` tags within user or tool messages. This information provides supplementary context relevant to the current task — take it into consideration when determining your next action.
-
-Tool results and user messages may also include `<system-reminder>` tags. Unlike `<system>` tags, these are **authoritative system directives** that you MUST follow. They bear no direct relation to the specific tool results or user messages in which they appear. Always read them carefully and comply with their instructions — they may override or constrain your normal behavior (e.g., restricting you to read-only actions during plan mode).
-
-If the `Shell`, `TaskList`, `TaskOutput`, and `TaskStop` tools are available and you are the root agent, you can use Background Bash for long-running shell commands. Launch it via `Shell` with `run_in_background=true` and a short `description`. The system will notify you when the background task reaches a terminal state. Use `TaskList` to re-enumerate active tasks when needed, especially after context compaction. Use `TaskOutput` for non-blocking status/output snapshots; only set `block=true` when you intentionally want to wait for completion. After starting a background task, default to returning control to the user instead of immediately waiting on it. Use `TaskStop` only when you need to cancel the task. For human users in the interactive shell, the only task-management slash command is `/task`. Do not tell users to run `/task list`, `/task output`, `/task stop`, `/tasks`, or any other invented slash subcommands. If you are a subagent or these tools are not available, do not assume you can create or control background tasks.
-
-If a foreground tool call or a background agent requests approval, the approval is coordinated through the unified approval runtime and surfaced through the root UI channel. Do not assume approvals are local to a single subagent turn.
-
-# General Guidelines for Coding
-
-When building something from scratch, you should:
-
-- Understand the user's requirements.
-- Ask the user for clarification if there is anything unclear.
-- Design the architecture and make a plan for the implementation.
-- Write the code in a modular and maintainable way.
-
-Always use tools to implement your code changes:
-
-- Use `WriteFile` to create or overwrite source files. Code that only appears in your text response is NOT saved to the file system and will not take effect.
-- Use `Shell` to run and test your code after writing it.
-- Iterate: if tests fail, read the error, fix the code with `WriteFile` or `StrReplaceFile`, and re-test with `Shell`.
-
-When working on an existing codebase, you should:
-
-- Understand the codebase by reading it with tools (`ReadFile`, `Glob`, `Grep`) before making changes. Identify the ultimate goal and the most important criteria to achieve the goal.
-- For a bug fix, you typically need to check error logs or failed tests, scan over the codebase to find the root cause, and figure out a fix. If user mentioned any failed tests, you should make sure they pass after the changes.
-- For a feature, you typically need to design the architecture, and write the code in a modular and maintainable way, with minimal intrusions to existing code. Add new tests if the project already has tests.
-- For a code refactoring, you typically need to update all the places that call the code you are refactoring if the interface changes. DO NOT change any existing logic especially in tests, focus only on fixing any errors caused by the interface changes.
-- Make MINIMAL changes to achieve the goal. This is very important to your performance.
-- Follow the coding style of existing code in the project.
-- For broader codebase exploration and deep research, use the `Agent` tool with `subagent_type="explore"`. This is a fast, read-only agent specialized for searching and understanding codebases. Use it when your task will clearly require more than 3 search queries, or when you need to investigate multiple files and patterns. You can launch multiple explore agents concurrently to investigate independent questions in parallel.
-
-Code quality defaults (unless project or domain rules override):
-
-- Keep functions focused, shallow, and easy to scan; prefer short lines, clear indentation, and early exits over deep nesting.
-- Use meaningful identifiers, avoid shadowing, and follow the language/context casing convention (`camelCase`, `snake_case`, `kebab-case`, or `PascalCase`).
-- Avoid duplicate logic in the same change, but do not invent broad abstractions for one-off repetition.
-- Comment only non-obvious algorithms, workarounds, business rules, or edge cases. Use `TODO:` for real technical debt; do not comment self-evident code.
-- Keep modules/classes cohesive and testable. Choose efficient data structures and transformations when they improve clarity or scaling.
-- Wrap error-prone I/O, API, network, and resource operations with appropriate error handling, timeouts/fallbacks, and cleanup.
-- Adapt to domain standards when relevant (for example stricter MISRA-style practices for critical C/C++ systems).
-
-DO NOT run `git commit`, `git push`, `git reset`, `git rebase` and/or do any other git mutations unless explicitly asked to do so. Ask for confirmation each time when you need to do git mutations, even if the user has confirmed in earlier conversations.
-
-# General Guidelines for Research and Data Processing
-
-The user may ask you to research on certain topics, process or generate certain multimedia files. When doing such tasks, you must:
-
-- Understand the user's requirements thoroughly, ask for clarification before you start if needed.
-- Make plans before doing deep or wide research, to ensure you are always on track.
-- Search on the Internet if possible, with carefully-designed search queries to improve efficiency and accuracy.
-- Use proper tools or shell commands or Python packages to process or generate images, videos, PDFs, docs, spreadsheets, presentations, or other multimedia files. Detect if there are already such tools in the environment. If you have to install third-party tools/packages, you MUST ensure that they are installed in a virtual/isolated environment.
-- Once you generate or edit any images, videos or other media files, try to read it again before proceed, to ensure that the content is as expected.
-- Avoid installing or deleting anything to/from outside of the current working directory. If you have to do so, ask the user for confirmation.
-
-# Working Environment
-
-## Operating System
-
-You are running on **macOS**. The Shell tool executes commands using **bash (`/bin/bash`)**.
-
-The operating environment is not in a sandbox. Any actions you do will immediately affect the user's system. So you MUST be extremely cautious. Unless being explicitly instructed to do so, you should never access (read/write/execute) files outside of the working directory.
-
-## Date and Time
-
-The current date and time in ISO format is `1970-01-01T00:00:00+00:00`. Treat this as the authoritative present — it reflects the real "now", which is later than your training data suggests. Anchor all reasoning about the current date, the year, recency, and what counts as the "latest" version or release to `1970-01-01T00:00:00+00:00`; do not fall back on an earlier year you might assume from training. Use it as your reference when searching the web or checking file modification times. If you need the exact time, use the Shell tool with a proper command.
-
-## Working Directory
-
-The current working directory is `/path/to/work/dir`. This should be considered as the project root if you are instructed to perform tasks on the project. Every file system operation will be relative to the working directory if you do not explicitly specify the absolute path. Tools may require absolute paths for some parameters, IF SO, YOU MUST use absolute paths for these parameters.
-
-The directory listing of current working directory is:
-
-```
-Test ls content
-```
-
-Use this as your basic understanding of the project structure. The tree only shows the first two levels; entries marked "... and N more" indicate additional contents — use Glob or Shell to explore further.
-
-# Project Information
-
-Markdown files named `AGENTS.md` usually contain the background, structure, coding styles, user preferences and other relevant information about the project. You should use this information to understand the project and the user's preferences. `AGENTS.md` files may exist at different locations in the project, but typically there is one in the project root.
-
-> Why `AGENTS.md`?
->
-> `README.md` files are for humans: quick starts, project descriptions, and contribution guidelines. `AGENTS.md` complements this by containing the extra, sometimes detailed context coding agents need: build steps, tests, and conventions that might clutter a README or aren’t relevant to human contributors.
->
-> We intentionally kept it separate to:
->
-> - Give agents a clear, predictable place for instructions.
-> - Keep `README`s concise and focused on human contributors.
-> - Provide precise, agent-focused guidance that complements existing `README` and docs.
-
-The `AGENTS.md` instructions (merged from all applicable directories):
-
-`````````
-Test agents content
-`````````
-
-The block above is authoritative and already merged for you: every `AGENTS.md` from the project root down to your working directory, with deeper (more specific) files overriding shallower ones. Each file governs its own directory and everything beneath it. Precedence, highest first: direct user instructions in this conversation, then deeper `AGENTS.md`, then shallower `AGENTS.md`.
-
-Treat the merged block above as complete for the project-root-to-working-directory range. Look for additional `AGENTS.md` files only in directories *below* your working directory: when you edit files there, apply any deeper `AGENTS.md` by the same precedence. `README`/`README.md` files are optional supplementary context, not instructions.
-
-If a change you make invalidates anything an `AGENTS.md` documents (build/test commands, conventions, structure, workflows), update that `AGENTS.md` in the same change so it stays trustworthy.
-
-# Skills
-
-Skills are reusable, composable capabilities that enhance your abilities. Each skill is a self-contained directory with a `SKILL.md` file that contains instructions, examples, and/or reference material.
-
-## What are skills?
-
-Skills are modular extensions that provide:
-
-- Specialized knowledge: Domain-specific expertise (e.g., PDF processing, data analysis)
-- Workflow patterns: Best practices for common tasks
-- Tool integrations: Pre-configured tool chains for specific operations
-- Reference material: Documentation, templates, and examples
-
-## Available skills
-
-Skills are grouped by scope (`Project`, `User`, `Extra`, `Built-in`) so you can tell where each came from. When the user refers to "the skill in this project" or "the user-scope skill", use the scope heading to disambiguate. When multiple scopes define a skill with the same name, the more specific scope takes precedence: **Project overrides User overrides Extra overrides Built-in**.
-
-No skills found.
-
-## How to use skills
-
-Identify the skills that are likely to be useful for the tasks you are currently working on, read the `SKILL.md` file for detailed instructions, guidelines, scripts and more. If a skill `<name>` has a companion `<name>-local`, treat `<name>-local` as local project specialization and apply it after the core skill.
-
-Only read skill details when needed to conserve the context window.
-
-# Output Formatting
-
-Your responses are rendered as Markdown in a terminal. Emit well-formed Markdown so it renders cleanly:
-
-- **Tables:** put the header row on its own line, the `|---|---|` delimiter row on the immediately following line (no blank line between them), and one row per line. Never glue a table onto adjacent prose (e.g. `Findings| Col |`) and never cram multiple rows onto one line. Leave a blank line before and after the table.
-- Prefer a short bullet list over a table when there are only a few items or any cell is long; reserve tables for genuinely tabular data with short cells.
-- **Code fences are for code only.** Use triple-backtick blocks tagged with a language (for example, `python` or `toml`) solely for source, config, or commands — one snippet per block. Never wrap a prose report, finding list, checklist, or ASCII box in a fence to align or frame it; write it as normal Markdown (headings, bullets, tables) so it renders cleanly.
-- **Status icons sparingly.** A check/cross/dot can mark a single headline result, but do not prefix every line with one. Use plain words for severity and outcomes (e.g. `High`, `PASS`, `0 findings`). The terminal renders icons as calm monochrome glyphs only outside code fences — another reason not to box reports.
-
-# Ultimate Reminders
-
-At any time, you should be HELPFUL, CONCISE, and ACCURATE. Be thorough in your actions — test what you build, verify what you change — not in your explanations.
-
-- Never diverge from the requirements and the goals of the task you work on. Stay on track.
-- Never give the user more than what they want.
-- Try your best to avoid any hallucination. Do fact checking before providing any factual information.
-- Think about the best approach, then take action decisively.
-- Do not give up too early.
-- ALWAYS, keep it stupidly simple. Do not overcomplicate things.
-- When the task requires creating or modifying files, always use tools to do so. Never treat displaying code in your response as a substitute for actually writing it to the file system.\
-"""
-    )
+    # Identity invariants — targeted checks so unrelated prompt edits don't break this test.
+    assert "## Product Identity" in agent.system_prompt
+    assert "Pythinker" in agent.system_prompt
+    assert "Pythoughts-labs" in agent.system_prompt
+    assert "Do not name or describe the underlying language model" in agent.system_prompt
 
     builtin_types = [
         (

From bbd7632f14e94b7c107f021ccc58eb2fbad483cb Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:40:17 -0400
Subject: [PATCH 20/28] chore(deps): add pytest-cov to all package dev
 dependency groups

---
 packages/pythinker-core/pyproject.toml |   1 +
 packages/pythinker-host/pyproject.toml |   1 +
 pyproject.toml                         |   1 +
 sdks/pythinker-sdk/pyproject.toml      |   1 +
 uv.lock                                | 106 +++++++++++++++++++++++++
 5 files changed, 110 insertions(+)

diff --git a/packages/pythinker-core/pyproject.toml b/packages/pythinker-core/pyproject.toml
index 21494054..1eaea6a0 100644
--- a/packages/pythinker-core/pyproject.toml
+++ b/packages/pythinker-core/pyproject.toml
@@ -49,6 +49,7 @@ dev = [
     "ty>=0.0.7",
     "pytest>=9.0.3",
     "pytest-asyncio>=1.3.0",
+    "pytest-cov>=6.0",
     "respx>=0.23.1",
     "ruff>=0.14.10",
     "inline-snapshot[black]>=0.31.1",
diff --git a/packages/pythinker-host/pyproject.toml b/packages/pythinker-host/pyproject.toml
index a2bafd8a..8a294efd 100644
--- a/packages/pythinker-host/pyproject.toml
+++ b/packages/pythinker-host/pyproject.toml
@@ -38,6 +38,7 @@ dev = [
     "ty>=0.0.7",
     "pytest>=9.0.3",
     "pytest-asyncio>=1.3.0",
+    "pytest-cov>=6.0",
     "ruff>=0.14.9",
 ]
 
diff --git a/pyproject.toml b/pyproject.toml
index 22e28803..a768ed2b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,6 +72,7 @@ dev = [
     "ty>=0.0.9",
     "pytest>=9.0.3",
     "pytest-asyncio>=1.3.0",
+    "pytest-cov>=6.0",
     "ruff>=0.14.10,<0.15",
 ]
 
diff --git a/sdks/pythinker-sdk/pyproject.toml b/sdks/pythinker-sdk/pyproject.toml
index 7a9d0cb5..e0239690 100644
--- a/sdks/pythinker-sdk/pyproject.toml
+++ b/sdks/pythinker-sdk/pyproject.toml
@@ -36,6 +36,7 @@ dev = [
     "ty>=0.0.7",
     "pytest>=9.0.3",
     "pytest-asyncio>=1.3.0",
+    "pytest-cov>=6.0",
     "ruff>=0.14.10",
 ]
 
diff --git a/uv.lock b/uv.lock
index 68aee74f..3d5c26c9 100644
--- a/uv.lock
+++ b/uv.lock
@@ -578,6 +578,90 @@ wheels = [
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 ]
 
+[[package]]
+name = "coverage"
+version = "7.14.1"
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+    { url = "https://files.pythonhosted.org/packages/e7/c5/9348fe40dbfd4991aaf78df2c6c3098bfb2cc834d1fd362a64b4efef855a/coverage-7.14.1-cp314-cp314t-musllinux_1_2_riscv64.whl", hash = "sha256:5ea0c297e27133853b4d8a3eb799bff5a2dbd9f2f41537a240d337ac9b4df890", size = 260896, upload-time = "2026-05-26T20:41:23.428Z" },
+    { url = "https://files.pythonhosted.org/packages/ca/92/1ea0f03929da7cf87206b1fa24f4c8e9c158be0455481af29ec0a1f3503f/coverage-7.14.1-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:01b7733daad0237daa01ef80fe2dfceffc911e6a17fa7b55d14aa8214eaaaecd", size = 263214, upload-time = "2026-05-26T20:41:25.419Z" },
+    { url = "https://files.pythonhosted.org/packages/f6/a9/b2493c054c0e01a643266742ab45e15744e60743f9260cd930c7142b1124/coverage-7.14.1-cp314-cp314t-win32.whl", hash = "sha256:6adc5a36984624a70bf11d7184e20fa0a49aa7c47ffab43804106a1a695ea22e", size = 223624, upload-time = "2026-05-26T20:41:27.795Z" },
+    { url = "https://files.pythonhosted.org/packages/fc/bd/3e1e6a57fccd2d7c83fcdf338e93ba98eb85c6e877dd34731ac585375490/coverage-7.14.1-cp314-cp314t-win_amd64.whl", hash = "sha256:ddf799247318f34dbcd2efa8c95a8d0642674e926bb1774cf9b63dfd2a389d1c", size = 224728, upload-time = "2026-05-26T20:41:30.098Z" },
+    { url = "https://files.pythonhosted.org/packages/bb/d7/31066cf1d2f0c6c797fce911bcfa01dd35642dc6da992a950256097c5860/coverage-7.14.1-cp314-cp314t-win_arm64.whl", hash = "sha256:145986fe66647eb489f18d9a997567a3fd358584c4b5a808769113abc07466af", size = 222752, upload-time = "2026-05-26T20:41:32.123Z" },
+    { url = "https://files.pythonhosted.org/packages/8a/3c/1a983b9a745d7f83d53f057bcc5bf79ba6a2bbc08266b3f0c7d6fe630c9b/coverage-7.14.1-py3-none-any.whl", hash = "sha256:a252f21c27e38347e60111a3266b03827422a7d5525951aceee313aa68bab1d2", size = 211815, upload-time = "2026-05-26T20:41:34.078Z" },
+]
+
 [[package]]
 name = "cryptography"
 version = "48.0.0"
@@ -2415,6 +2499,20 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/e5/35/f8b19922b6a25bc0880171a2f1a003eaeb93657475193ab516fd87cac9da/pytest_asyncio-1.3.0-py3-none-any.whl", hash = "sha256:611e26147c7f77640e6d0a92a38ed17c3e9848063698d5c93d5aa7aa11cebff5", size = 15075, upload-time = "2025-11-10T16:07:45.537Z" },
 ]
 
+[[package]]
+name = "pytest-cov"
+version = "7.1.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "coverage" },
+    { name = "pluggy" },
+    { name = "pytest" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/b1/51/a849f96e117386044471c8ec2bd6cfebacda285da9525c9106aeb28da671/pytest_cov-7.1.0.tar.gz", hash = "sha256:30674f2b5f6351aa09702a9c8c364f6a01c27aae0c1366ae8016160d1efc56b2", size = 55592, upload-time = "2026-03-21T20:11:16.284Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/9d/7a/d968e294073affff457b041c2be9868a40c1c71f4a35fcc1e45e5493067b/pytest_cov-7.1.0-py3-none-any.whl", hash = "sha256:a0461110b7865f9a271aa1b51e516c9a95de9d696734a2f71e3e78f46e1d4678", size = 22876, upload-time = "2026-03-21T20:11:14.438Z" },
+]
+
 [[package]]
 name = "pythinker-code"
 version = "0.32.0"
@@ -2465,6 +2563,7 @@ dev = [
     { name = "pyright" },
     { name = "pytest" },
     { name = "pytest-asyncio" },
+    { name = "pytest-cov" },
     { name = "ruff" },
     { name = "ty" },
 ]
@@ -2516,6 +2615,7 @@ dev = [
     { name = "pyright", specifier = ">=1.1.409" },
     { name = "pytest", specifier = ">=9.0.3" },
     { name = "pytest-asyncio", specifier = ">=1.3.0" },
+    { name = "pytest-cov", specifier = ">=6.0" },
     { name = "ruff", specifier = ">=0.14.10,<0.15" },
     { name = "ty", specifier = ">=0.0.9" },
 ]
@@ -2549,6 +2649,7 @@ dev = [
     { name = "pyright" },
     { name = "pytest" },
     { name = "pytest-asyncio" },
+    { name = "pytest-cov" },
     { name = "respx" },
     { name = "ruff" },
     { name = "ty" },
@@ -2577,6 +2678,7 @@ dev = [
     { name = "pyright", specifier = ">=1.1.407" },
     { name = "pytest", specifier = ">=9.0.3" },
     { name = "pytest-asyncio", specifier = ">=1.3.0" },
+    { name = "pytest-cov", specifier = ">=6.0" },
     { name = "respx", specifier = ">=0.23.1" },
     { name = "ruff", specifier = ">=0.14.10" },
     { name = "ty", specifier = ">=0.0.7" },
@@ -2597,6 +2699,7 @@ dev = [
     { name = "pyright" },
     { name = "pytest" },
     { name = "pytest-asyncio" },
+    { name = "pytest-cov" },
     { name = "ruff" },
     { name = "ty" },
 ]
@@ -2613,6 +2716,7 @@ dev = [
     { name = "pyright", specifier = ">=1.1.407" },
     { name = "pytest", specifier = ">=9.0.3" },
     { name = "pytest-asyncio", specifier = ">=1.3.0" },
+    { name = "pytest-cov", specifier = ">=6.0" },
     { name = "ruff", specifier = ">=0.14.9" },
     { name = "ty", specifier = ">=0.0.7" },
 ]
@@ -2674,6 +2778,7 @@ dev = [
     { name = "pyright" },
     { name = "pytest" },
     { name = "pytest-asyncio" },
+    { name = "pytest-cov" },
     { name = "ruff" },
     { name = "ty" },
 ]
@@ -2693,6 +2798,7 @@ dev = [
     { name = "pyright", specifier = ">=1.1.407" },
     { name = "pytest", specifier = ">=9.0.3" },
     { name = "pytest-asyncio", specifier = ">=1.3.0" },
+    { name = "pytest-cov", specifier = ">=6.0" },
     { name = "ruff", specifier = ">=0.14.10" },
     { name = "ty", specifier = ">=0.0.7" },
 ]

From 52f5665707c305c3e11dd625c323970604b89c1d Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:42:33 -0400
Subject: [PATCH 21/28] chore(coverage): add [tool.coverage.*] config to all
 packages

---
 packages/pythinker-core/pyproject.toml | 16 ++++++++++++++++
 packages/pythinker-host/pyproject.toml | 16 ++++++++++++++++
 pyproject.toml                         | 16 ++++++++++++++++
 sdks/pythinker-sdk/pyproject.toml      | 16 ++++++++++++++++
 4 files changed, 64 insertions(+)

diff --git a/packages/pythinker-core/pyproject.toml b/packages/pythinker-core/pyproject.toml
index 1eaea6a0..b0126220 100644
--- a/packages/pythinker-core/pyproject.toml
+++ b/packages/pythinker-core/pyproject.toml
@@ -101,3 +101,19 @@ include = [
     "src/**/*.py",
     "tests/**/*.py",
 ]
+
+[tool.coverage.run]
+source_pkgs = ["pythinker_core"]
+branch = true
+relative_files = true
+
+[tool.coverage.report]
+show_missing = true
+skip_empty = true
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+    "@(abc\\.)?abstractmethod",
+    "\\.\\.\\.",
+]
diff --git a/packages/pythinker-host/pyproject.toml b/packages/pythinker-host/pyproject.toml
index 8a294efd..bbf57ad0 100644
--- a/packages/pythinker-host/pyproject.toml
+++ b/packages/pythinker-host/pyproject.toml
@@ -79,3 +79,19 @@ include = [
     "src/**/*.py",
     "tests/**/*.py",
 ]
+
+[tool.coverage.run]
+source_pkgs = ["pythinker_host"]
+branch = true
+relative_files = true
+
+[tool.coverage.report]
+show_missing = true
+skip_empty = true
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+    "@(abc\\.)?abstractmethod",
+    "\\.\\.\\.",
+]
diff --git a/pyproject.toml b/pyproject.toml
index a768ed2b..54136d2f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -189,3 +189,19 @@ updat = "updat"
 examin = "examin"
 continu = "continu"
 
+[tool.coverage.run]
+source_pkgs = ["pythinker_code"]
+branch = true
+relative_files = true
+
+[tool.coverage.report]
+show_missing = true
+skip_empty = true
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+    "@(abc\\.)?abstractmethod",
+    "\\.\\.\\.",
+]
+
diff --git a/sdks/pythinker-sdk/pyproject.toml b/sdks/pythinker-sdk/pyproject.toml
index e0239690..48abfe2a 100644
--- a/sdks/pythinker-sdk/pyproject.toml
+++ b/sdks/pythinker-sdk/pyproject.toml
@@ -71,3 +71,19 @@ python-version = "3.14"
 
 [tool.ty.src]
 include = ["src/**/*.py", "tests/**/*.py"]
+
+[tool.coverage.run]
+source_pkgs = ["pythinker_sdk"]
+branch = true
+relative_files = true
+
+[tool.coverage.report]
+show_missing = true
+skip_empty = true
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+    "@(abc\\.)?abstractmethod",
+    "\\.\\.\\.",
+]

From fba87d4f0eed1870ec26627c998afd94b830461d Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:44:43 -0400
Subject: [PATCH 22/28] chore(coverage): add cov-* Makefile targets and
 gitignore coverage artifacts

---
 .gitignore |  6 ++++++
 Makefile   | 20 ++++++++++++++++++++
 2 files changed, 26 insertions(+)

diff --git a/.gitignore b/.gitignore
index ddaeb858..7ab3576d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -70,3 +70,9 @@ blackbox/
 .pythinker-review/
 # pythinker — local agent state (do not commit)
 .pythinker-review-flow/
+
+# Coverage artifacts
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
diff --git a/Makefile b/Makefile
index a27fb75b..e55076dd 100644
--- a/Makefile
+++ b/Makefile
@@ -124,6 +124,26 @@ test-pythinker-review: ## Run pythinker-review tests.
 test-pythinker-sdk: ## Run pythinker-sdk tests.
 	@echo "==> Running pythinker-sdk tests"
 	@uv run --directory sdks/pythinker-sdk pytest tests -vv
+
+.PHONY: cov cov-pythinker-code cov-pythinker-core cov-pythinker-host cov-pythinker-sdk
+cov: cov-pythinker-code cov-pythinker-core cov-pythinker-host cov-pythinker-sdk ## Run all test suites with coverage.
+cov-pythinker-code: ## Run Pythinker Code tests with coverage.
+	@echo "==> Running Pythinker Code tests with coverage"
+	@uv run pytest tests tests_e2e \
+		--cov --cov-report=xml:coverage.xml --cov-report=term-missing -vv
+cov-pythinker-core: ## Run Pythinker Core tests with coverage.
+	@echo "==> Running Pythinker Core tests with coverage"
+	@uv run --directory packages/pythinker-core pytest --doctest-modules \
+		--cov --cov-report=xml:coverage.xml -vv
+cov-pythinker-host: ## Run Pythinker Host tests with coverage.
+	@echo "==> Running Pythinker Host tests with coverage"
+	@uv run --directory packages/pythinker-host pytest tests \
+		--cov --cov-report=xml:coverage.xml -vv
+cov-pythinker-sdk: ## Run Pythinker SDK tests with coverage.
+	@echo "==> Running Pythinker SDK tests with coverage"
+	@uv run --directory sdks/pythinker-sdk pytest tests \
+		--cov --cov-report=xml:coverage.xml -vv
+
 .PHONY: build build-pythinker-code build-pythinker-core build-pythinker-host build-pythinker-review build-pythinker-sdk build-bin build-bin-onedir
 build: build-web build-vis build-pythinker-code build-pythinker-core build-pythinker-host build-pythinker-review build-pythinker-sdk ## Build Python packages for release.
 build-pythinker-code: build-web build-vis ## Build the pythinker-code sdist and wheel.

From 5a9efa48bfcd0ab6b9e7e085bf1af0e5a270e6bb Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:46:06 -0400
Subject: [PATCH 23/28] ci(codecov): add codecov.yml with per-package flags and
 informational thresholds

---
 codecov.yml | 58 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 codecov.yml

diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 00000000..9b3f9ead
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,58 @@
+codecov:
+  notify:
+    after_n_builds: 3
+    wait_for_ci: true
+
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+
+comment:
+  layout: "diff, flags, files"
+  behavior: default
+  require_changes: true
+  show_carryforward_flags: true
+
+flag_management:
+  default_rules:
+    carryforward: true
+    statuses:
+      - type: project
+        informational: true
+      - type: patch
+        informational: true
+  individual_flags:
+    - name: pythinker-code
+      paths:
+        - src/pythinker_code/
+      after_n_builds: 3
+    - name: pythinker-core
+      paths:
+        - packages/pythinker-core/src/pythinker_core/
+      after_n_builds: 3
+    - name: pythinker-host
+      paths:
+        - packages/pythinker-host/src/pythinker_host/
+      after_n_builds: 3
+    - name: pythinker-sdk
+      paths:
+        - sdks/pythinker-sdk/src/pythinker_sdk/
+      after_n_builds: 3
+
+ignore:
+  - "**/tests/**"
+  - "**/tests_e2e/**"
+  - "**/tests_ai/**"
+  - "**/conftest.py"
+  - "**/__init__.py"
+  - "src/pythinker_code/deps/**"
+  - "examples/**"

From 1efe5977447260a183f0df564932c3320dbac3b4 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:47:04 -0400
Subject: [PATCH 24/28] ci(codecov): add coverage upload to pythinker-code CI

---
 .github/workflows/ci-pythinker-cli.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-pythinker-cli.yml b/.github/workflows/ci-pythinker-cli.yml
index d6bbac8a..43d94842 100644
--- a/.github/workflows/ci-pythinker-cli.yml
+++ b/.github/workflows/ci-pythinker-cli.yml
@@ -90,7 +90,16 @@ jobs:
         env:
           UV_PYTHON: ${{ steps.setup-python.outputs.python-path }}
           PYTHONUTF8: "1"
-        run: make test-pythinker-code
+        run: make cov-pythinker-code
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: pythinker-code
+          name: pythinker-code-${{ matrix.python-version }}
+          fail_ci_if_error: false
 
   build:
     strategy:

From 592fd4631d64e26840e7e99e29b64e8bdfacab7b Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:47:53 -0400
Subject: [PATCH 25/28] ci(codecov): add coverage upload to pythinker-core CI

---
 .github/workflows/ci-pythinker-core.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-pythinker-core.yml b/.github/workflows/ci-pythinker-core.yml
index db96fe36..c764632a 100644
--- a/.github/workflows/ci-pythinker-core.yml
+++ b/.github/workflows/ci-pythinker-core.yml
@@ -57,7 +57,16 @@ jobs:
       - name: Run tests
         env:
           UV_PYTHON: ${{ steps.setup-python.outputs.python-path }}
-        run: make test-pythinker-core
+        run: make cov-pythinker-core
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: packages/pythinker-core/coverage.xml
+          flags: pythinker-core
+          name: pythinker-core-${{ matrix.python-version }}
+          fail_ci_if_error: false
 
   docs:
     runs-on: ubuntu-latest

From a8ba74b56351b2117e614c8ab8fe7334ffd2bac2 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:48:53 -0400
Subject: [PATCH 26/28] ci(codecov): add coverage upload to pythinker-host CI
 (ubuntu-22.04 only)

---
 .github/workflows/ci-pythinker-host.yml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-pythinker-host.yml b/.github/workflows/ci-pythinker-host.yml
index b74c7133..21a62660 100644
--- a/.github/workflows/ci-pythinker-host.yml
+++ b/.github/workflows/ci-pythinker-host.yml
@@ -112,4 +112,14 @@ jobs:
       - name: Run tests
         env:
           UV_PYTHON: ${{ steps.setup-python.outputs.python-path }}
-        run: make test-pythinker-host
+        run: make cov-pythinker-host
+
+      - name: Upload coverage to Codecov
+        if: matrix.runner == 'ubuntu-22.04'
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: packages/pythinker-host/coverage.xml
+          flags: pythinker-host
+          name: pythinker-host-${{ matrix.python-version }}
+          fail_ci_if_error: false

From c07c43a0a33f70aab69aa9d0962b53c9d7571c5e Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:49:39 -0400
Subject: [PATCH 27/28] ci(codecov): add coverage upload to pythinker-sdk CI

---
 .github/workflows/ci-pythinker-sdk.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-pythinker-sdk.yml b/.github/workflows/ci-pythinker-sdk.yml
index fea0aa64..e9d97b5d 100644
--- a/.github/workflows/ci-pythinker-sdk.yml
+++ b/.github/workflows/ci-pythinker-sdk.yml
@@ -57,7 +57,16 @@ jobs:
       - name: Run tests
         env:
           UV_PYTHON: ${{ steps.setup-python.outputs.python-path }}
-        run: make test-pythinker-sdk
+        run: make cov-pythinker-sdk
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: sdks/pythinker-sdk/coverage.xml
+          flags: pythinker-sdk
+          name: pythinker-sdk-${{ matrix.python-version }}
+          fail_ci_if_error: false
 
   docs:
     runs-on: ubuntu-latest

From e97444ecfae071f98889fb3ced12bb216aef3787 Mon Sep 17 00:00:00 2001
From: mohamed-elkholy95 <melkholy@techmatrix.com>
Date: Wed, 3 Jun 2026 16:50:58 -0400
Subject: [PATCH 28/28] ci(security): pin codecov-action to commit SHA

---
 .github/workflows/ci-pythinker-cli.yml  | 2 +-
 .github/workflows/ci-pythinker-core.yml | 2 +-
 .github/workflows/ci-pythinker-host.yml | 2 +-
 .github/workflows/ci-pythinker-sdk.yml  | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-pythinker-cli.yml b/.github/workflows/ci-pythinker-cli.yml
index 43d94842..e2550f80 100644
--- a/.github/workflows/ci-pythinker-cli.yml
+++ b/.github/workflows/ci-pythinker-cli.yml
@@ -93,7 +93,7 @@ jobs:
         run: make cov-pythinker-code
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml
diff --git a/.github/workflows/ci-pythinker-core.yml b/.github/workflows/ci-pythinker-core.yml
index c764632a..abeb0541 100644
--- a/.github/workflows/ci-pythinker-core.yml
+++ b/.github/workflows/ci-pythinker-core.yml
@@ -60,7 +60,7 @@ jobs:
         run: make cov-pythinker-core
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: packages/pythinker-core/coverage.xml
diff --git a/.github/workflows/ci-pythinker-host.yml b/.github/workflows/ci-pythinker-host.yml
index 21a62660..1d83abde 100644
--- a/.github/workflows/ci-pythinker-host.yml
+++ b/.github/workflows/ci-pythinker-host.yml
@@ -116,7 +116,7 @@ jobs:
 
       - name: Upload coverage to Codecov
         if: matrix.runner == 'ubuntu-22.04'
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: packages/pythinker-host/coverage.xml
diff --git a/.github/workflows/ci-pythinker-sdk.yml b/.github/workflows/ci-pythinker-sdk.yml
index e9d97b5d..bb418a7f 100644
--- a/.github/workflows/ci-pythinker-sdk.yml
+++ b/.github/workflows/ci-pythinker-sdk.yml
@@ -60,7 +60,7 @@ jobs:
         run: make cov-pythinker-sdk
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: sdks/pythinker-sdk/coverage.xml