chore: release v3.1.5

CHANGELOG.md

@@ -2,6 +2,34 @@
 
 All notable changes to this project will be documented in this file. See [commit-and-tag-version](https://github.com/absolute-version/commit-and-tag-version) for commit guidelines.
 
+## [3.1.5](https://github.com/optave/codegraph/compare/v3.1.4...v3.1.5) (2026-03-16)
+
+**Phase 3 architectural refactoring completes.** This release finishes the remaining two Phase 3 roadmap tasks — domain directory grouping (3.15) and CLI composability (3.16) — bringing Phase 3 to 14 of 14 tasks complete. The `src/` directory is now reorganized into `domain/`, `features/`, and `presentation/` layers. A new `openGraph()` helper eliminates DB-open/close boilerplate across CLI commands, and a universal output formatter adds `--table` and `--csv` output to all commands. Several post-reorganization bugs are fixed: complexity/CFG/dataflow analysis restored after the move, MCP server imports corrected, worktree boundary escapes prevented, CJS `require()` support added, and LIKE wildcard injection in queries patched.
+
+### Features
+
+* **cli:** `openGraph()` helper and universal output formatter with `--table` and `--csv` output formats — eliminates per-command DB boilerplate and format-switching logic ([#461](https://github.com/optave/codegraph/pull/461))
+
+### Bug Fixes
+
+* **builder:** restore complexity/CFG/dataflow analysis that silently stopped running after src/ reorganization ([#469](https://github.com/optave/codegraph/pull/469))
+* **db:** prevent `findDbPath` from escaping git worktree boundary — stops codegraph from accidentally using a parent repo's database ([#457](https://github.com/optave/codegraph/pull/457))
+* **mcp:** update MCP server import path after src/ reorganization ([#466](https://github.com/optave/codegraph/pull/466))
+* **api:** add CJS `require()` support to package exports — fixes `ERR_REQUIRE_ESM` for CommonJS consumers ([#472](https://github.com/optave/codegraph/pull/472))
+* **db:** escape LIKE wildcards in `NodeQuery.fileFilter` and `nameLike` — prevents filenames containing `%` or `_` from matching unrelated rows ([#446](https://github.com/optave/codegraph/pull/446))
+
+### Refactors
+
+* **architecture:** reorganize `src/` into `domain/`, `features/`, `presentation/` layers — completes Phase 3.15 domain directory grouping ([#456](https://github.com/optave/codegraph/pull/456))
+* **architecture:** move remaining flat `src/` files into subdirectories ([#458](https://github.com/optave/codegraph/pull/458))
+* **architecture:** resolve three post-reorganization issues (circular imports, barrel exports, path corrections) ([#459](https://github.com/optave/codegraph/pull/459))
+* **queries:** deduplicate BFS impact traversal and centralize config loading ([#463](https://github.com/optave/codegraph/pull/463))
+* **tests:** migrate integration tests to InMemoryRepository for faster execution ([#462](https://github.com/optave/codegraph/pull/462))
+
+### Tests
+
+* **db:** add `findRepoRoot` and `findDbPath` ceiling boundary tests ([#475](https://github.com/optave/codegraph/pull/475))
+
 ## [3.1.4](https://github.com/optave/codegraph/compare/v3.1.3...v3.1.4) (2026-03-16)
 
 **Phase 3 architectural refactoring reaches near-completion.** This release delivers 11 of 14 roadmap tasks in Phase 3 (Vertical Slice Architecture), restructuring the codebase from a flat collection of large files into a modular subsystem layout. The 3,395-line `queries.js` is decomposed into `src/analysis/` and `src/shared/` modules. The MCP tool registry becomes composable. CLI commands are self-contained modules under `src/commands/`. A domain error hierarchy replaces ad-hoc throws. The build pipeline is decomposed into named stages. The embedder is extracted into `src/embeddings/` with pluggable stores and search strategies. A unified graph model (`src/graph/`) consolidates four parallel graph representations. Nodes gain qualified names, hierarchical scoping, and visibility metadata. An `InMemoryRepository` enables fast unit testing without SQLite. The presentation layer (`src/presentation/`) separates all output formatting from domain logic. `better-sqlite3` is bumped to 12.8.0.

README.md

@@ -477,6 +477,8 @@ codegraph registry remove <name>  # Unregister
 | `-f, --file <path>` | Scope to a specific file (`fn`, `context`, `where`) |
 | `--mode <mode>` | Search mode: `hybrid` (default), `semantic`, or `keyword` (`search`) |
 | `--ndjson` | Output as newline-delimited JSON (one object per line) |
+| `--table` | Output as auto-column aligned table |
+| `--csv` | Output as CSV (RFC 4180, nested objects flattened) |
 | `--limit <n>` | Limit number of results |
 | `--offset <n>` | Skip first N results (pagination) |
 | `--rrf-k <n>` | RRF smoothing constant for multi-query search (default 60) |
@@ -775,7 +777,7 @@ See **[ROADMAP.md](docs/roadmap/ROADMAP.md)** for the full development roadmap a
 1. ~~**Rust Core**~~ — **Complete** (v1.3.0) — native tree-sitter parsing via napi-rs, parallel multi-core parsing, incremental re-parsing, import resolution & cycle detection in Rust
 2. ~~**Foundation Hardening**~~ — **Complete** (v1.4.0) — parser registry, 12-tool MCP server with multi-repo support, test coverage 62%→75%, `apiKeyCommand` secret resolution, global repo registry
 3. ~~**Deep Analysis**~~ — **Complete** (v3.0.0) — dataflow analysis (flows_to, returns, mutates), intraprocedural CFG for all 11 languages, stored AST nodes, expanded node/edge types (parameter, property, constant, contains, parameter_of, receiver), GraphML/GraphSON/Neo4j CSV export, interactive HTML viewer, CLI consolidation, stable JSON schema
-4. **Architectural Refactoring** — **In Progress** (v3.1.4) — unified AST analysis, composable MCP, domain errors, builder pipeline, embedder subsystem, graph model, qualified names, presentation layer, InMemoryRepository (11/14 tasks complete)
+4. ~~**Architectural Refactoring**~~ — **Complete** (v3.1.5) — unified AST analysis, composable MCP, domain errors, builder pipeline, embedder subsystem, graph model, qualified names, presentation layer, InMemoryRepository, domain directory grouping, CLI composability
 5. **Natural Language Queries** — `codegraph ask` command, conversational sessions
 6. **Expanded Language Support** — 8 new languages (12 → 20)
 7. **GitHub Integration & CI** — reusable GitHub Action, PR review, SARIF output

docs/roadmap/ROADMAP.md

@@ -1,6 +1,6 @@
 # Codegraph Roadmap
 
-> **Current version:** 3.1.4 | **Status:** Active development | **Updated:** March 2026
+> **Current version:** 3.1.5 | **Status:** Active development | **Updated:** March 2026
 
 Codegraph is a strong local-first code graph CLI. This roadmap describes planned improvements across eleven phases -- closing gaps with commercial code intelligence platforms while preserving codegraph's core strengths: fully local, open source, zero cloud dependency by default.
 
@@ -16,7 +16,7 @@ Codegraph is a strong local-first code graph CLI. This roadmap describes planned
 | [**2**](#phase-2--foundation-hardening) | Foundation Hardening | Parser registry, complete MCP, test coverage, enhanced config, multi-repo MCP | **Complete** (v1.5.0) |
 | [**2.5**](#phase-25--analysis-expansion) | Analysis Expansion | Complexity metrics, community detection, flow tracing, co-change, manifesto, boundary rules, check, triage, audit, batch, hybrid search | **Complete** (v2.7.0) |
 | [**2.7**](#phase-27--deep-analysis--graph-enrichment) | Deep Analysis & Graph Enrichment | Dataflow analysis, intraprocedural CFG, AST node storage, expanded node/edge types, extractors refactoring, CLI consolidation, interactive viewer, exports command, normalizeSymbol | **Complete** (v3.0.0) |
-| [**3**](#phase-3--architectural-refactoring) | Architectural Refactoring (Vertical Slice) | Unified AST analysis framework, command/query separation, repository pattern, queries.js decomposition, composable MCP, CLI commands, domain errors, builder pipeline, presentation layer, domain grouping, curated API, unified graph model, qualified names, CLI composability | **In Progress** (v3.1.4) |
+| [**3**](#phase-3--architectural-refactoring) | Architectural Refactoring (Vertical Slice) | Unified AST analysis framework, command/query separation, repository pattern, queries.js decomposition, composable MCP, CLI commands, domain errors, builder pipeline, presentation layer, domain grouping, curated API, unified graph model, qualified names, CLI composability | **Complete** (v3.1.5) |
 | [**4**](#phase-4--native-analysis-acceleration) | Native Analysis Acceleration | Move JS-only build phases (AST nodes, CFG, dataflow, insert nodes, structure, roles, complexity) to Rust; fix incremental rebuild data loss on native; sub-100ms 1-file rebuilds | Planned |
 | [**5**](#phase-5--typescript-migration) | TypeScript Migration | Project setup, core type definitions, leaf -> core -> orchestration module migration, test migration, supply-chain security, CI coverage gates | Planned |
 | [**6**](#phase-6--runtime--extensibility) | Runtime & Extensibility | Event-driven pipeline, unified engine strategy, subgraph export filtering, transitive confidence, query caching, configuration profiles, pagination, plugin system, DX & onboarding | Planned |
@@ -556,14 +556,12 @@ Plus updated enums on existing tools (edge_kinds, symbol kinds).
 
 ---
 
-## Phase 3 -- Architectural Refactoring 🔄
+## Phase 3 -- Architectural Refactoring ✅
 
-> **Status:** In Progress -- started in v3.1.1
+> **Status:** Complete -- started in v3.1.1, finished in v3.1.5
 
 **Goal:** Restructure the codebase for modularity, testability, and long-term maintainability. These are internal improvements -- no new user-facing features, but they make every subsequent phase easier to build and maintain.
 
-> Reference: [generated/architecture.md](../../generated/architecture.md) -- full analysis with code examples and rationale.
-
 **Architecture pattern: Vertical Slice Architecture.** Each CLI command is a natural vertical slice — thin command entry point → domain logic → data access → formatted output. This avoids the overhead of layered patterns (Hexagonal, Clean Architecture) that would create abstractions with only one implementation, while giving clear boundaries and independent testability per feature. The target end-state directory structure:
 
 ```
@@ -960,34 +958,34 @@ src/
 
 **Affected files:** `src/viewer.js`, `src/export.js`, `src/sequence.js`, `src/infrastructure/result-formatter.js`
 
-### 3.15 -- Domain Directory Grouping
+### 3.15 -- Domain Directory Grouping ✅
 
-Once 3.2-3.4 are complete and analysis modules are standalone, group them under `src/domain/` by feature area. This is a move-only refactor — no logic changes, just directory organization to match the vertical slice target structure.
+**Completed:** `src/` reorganized into `domain/`, `features/`, and `presentation/` layers ([#456](https://github.com/optave/codegraph/pull/456), [#458](https://github.com/optave/codegraph/pull/458)). Three post-reorganization issues (circular imports, barrel exports, path corrections) resolved in [#459](https://github.com/optave/codegraph/pull/459). MCP server import path fixed in [#466](https://github.com/optave/codegraph/pull/466). Complexity/CFG/dataflow analysis restored after the move in [#469](https://github.com/optave/codegraph/pull/469).
 
 ```
 src/domain/
-  graph/                 # builder.js, resolve.js, cycles.js, watcher.js
+  graph/                 # builder.js, resolve.js, cycles.js, watcher.js, journal.js, change-journal.js
   analysis/              # symbol-lookup.js, impact.js, dependencies.js, module-map.js,
-                         # context.js, exports.js, roles.js (from 3.4 decomposition)
-  search/                # embedder.js subsystem (from 3.10)
+                         # context.js, exports.js, roles.js
+  search/                # embedder subsystem (models, generator, stores, search strategies)
+  parser.js              # tree-sitter WASM wrapper + LANGUAGE_REGISTRY
+  queries.js             # Query functions (symbol search, file deps, impact analysis)
 ```
 
-- 🔲 Move builder pipeline modules to `domain/graph/`
-- 🔲 Move decomposed query modules (from 3.4) to `domain/analysis/`
-- 🔲 Move embedder subsystem (from 3.10) to `domain/search/`
-- 🔲 Update all import paths across codebase
-- 🔲 Update `package.json` exports map (from 3.7)
+- ✅ Move builder pipeline modules to `domain/graph/` ([#456](https://github.com/optave/codegraph/pull/456))
+- ✅ Move decomposed query modules (from 3.4) to `domain/analysis/` ([#456](https://github.com/optave/codegraph/pull/456))
+- ✅ Move embedder subsystem (from 3.10) to `domain/search/` ([#456](https://github.com/optave/codegraph/pull/456))
+- ✅ Move remaining flat files (`features/`, `presentation/`, `infrastructure/`, `shared/`) into subdirectories ([#458](https://github.com/optave/codegraph/pull/458))
+- ✅ Update all import paths across codebase ([#456](https://github.com/optave/codegraph/pull/456), [#458](https://github.com/optave/codegraph/pull/458), [#459](https://github.com/optave/codegraph/pull/459))
 
 **Prerequisite:** 3.2, 3.4, 3.9, 3.10 should be complete before this step — it organizes the results of those decompositions.
 
-### 3.16 -- CLI Composability
-
-Practical cleanup to make the CLI surface match the internal composability that `*Data()` functions and MCP already provide. Not a philosophical overhaul -- just eliminating duplication and making the human CLI path as clean as the programmatic one.
+### 3.16 -- CLI Composability ✅
 
-**Context:** The internal architecture is already well-layered -- pure `*Data()` functions, read/write separation, NDJSON support. The 3.6 refactor split the former 1,525-line `cli.js` into `src/cli/` with 40 command modules and an 8-line thin wrapper, but individual commands still repeat DB open/close boilerplate, and output formatting is scattered across command files. MCP and `batch_query` already solve in-process composition for AI agents; these items fix the equivalent gaps on the CLI side.
+**Completed:** `openGraph(opts)` helper eliminates DB-open/close boilerplate across CLI commands. `resolveQueryOpts(opts)` extracts the 5 repeated option fields into one call, refactoring 20 command files. Universal output formatter extended with `--table` (auto-column aligned) and `--csv` (RFC 4180 with nested object flattening) output formats ([#461](https://github.com/optave/codegraph/pull/461)).
 
-- **Extract shared `openGraph()` helper.** The thin dispatcher is done (3.6), but each of the 40 `commands/*.js` files still inlines its own DB-open / config-load / cleanup sequence. A single `openGraph(opts)` helper returning `{ db, rootDir, config }` with engine selection, config loading, and cleanup eliminates ~200 lines of per-command duplication.
-- **Universal output formatter.** Complete the existing `result-formatter.js` into a full presentation layer that handles `--json`, `--ndjson`, `--table`, `--csv` for any data function. Commands produce data; the formatter renders. Eliminates per-command format-switching logic.
+- ✅ **`openGraph()` helper** — single helper returning `{ db, rootDir, config }` with engine selection, config loading, and cleanup ([#461](https://github.com/optave/codegraph/pull/461))
+- ✅ **Universal output formatter** — `outputResult()` extended with `--table` and `--csv` formats; `resolveQueryOpts()` extracts repeated option fields ([#461](https://github.com/optave/codegraph/pull/461))
 
 **Affected files:** `src/cli/commands/*.js`, `src/cli/shared/`, `src/presentation/result-formatter.js`