feat(config): three-scope config resolution (User → Project → Local)

.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@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          flags: pythinker-code
+          name: pythinker-code-${{ matrix.python-version }}
+          fail_ci_if_error: false
 
   build:
     strategy:

.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@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
+        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

.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@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
+        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

.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@75cd11691c0faa626561e295848008c8a7dddffe # pinned from v5.5.4
+        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

.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/

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.

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.

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/**"

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",
@@ -100,3 +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",
+    "\\.\\.\\.",
+]

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",
 ]
 
@@ -78,3 +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",
+    "\\.\\.\\.",
+]

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",
@@ -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",
 ]
 
@@ -188,3 +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",
+    "\\.\\.\\.",
+]
+

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",
 ]
 
@@ -70,3 +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",
+    "\\.\\.\\.",
+]

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"}:

src/pythinker_code/agents/default/system.md

@@ -1,4 +1,12 @@
-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
 

src/pythinker_code/cli/info.py

@@ -9,18 +9,20 @@
 
 class InfoData(TypedDict):
     pythinker_code_version: str
+    organization: str
     agent_spec_versions: list[str]
     wire_protocol_version: str
     python_version: str
 
 
 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']}",