codebase-context 1.6.2 → 1.8.0

package/dist/utils/usage-tracker.js

@@ -466,6 +466,8 @@ export class InternalFileGraph {
     exports = new Map();
     // Map: normalized file path -> Set of what symbols are imported from this file
     importedSymbols = new Map();
+    // Map: fromFile -> toFile -> edge details (line/symbols)
+    importDetails = new Map();
     // Root path for relative path conversion
     rootPath;
     constructor(rootPath) {
@@ -494,7 +496,7 @@ export class InternalFileGraph {
      * Track that importingFile imports importedFile
      * Both should be absolute paths; they will be normalized internally.
      */
-    trackImport(importingFile, importedFile, importedSymbols) {
+    trackImport(importingFile, importedFile, line, importedSymbols) {
         const fromFile = this.normalizePath(importingFile);
         const toFile = this.normalizePath(importedFile);
         // Initialize if needed
@@ -502,15 +504,35 @@ export class InternalFileGraph {
             this.imports.set(fromFile, new Set());
         }
         this.imports.get(fromFile).add(toFile);
-        // Track which symbols are imported from the target file
-        if (importedSymbols && importedSymbols.length > 0) {
+        const normalizedLine = typeof line === 'number' && Number.isFinite(line) && line > 0 ? Math.floor(line) : undefined;
+        const normalizedSymbols = importedSymbols && importedSymbols.length > 0
+            ? importedSymbols.filter((sym) => sym !== '*' && sym !== 'default')
+            : [];
+        if (normalizedLine || normalizedSymbols.length > 0) {
+            if (!this.importDetails.has(fromFile)) {
+                this.importDetails.set(fromFile, new Map());
+            }
+            const detailsForFrom = this.importDetails.get(fromFile);
+            const existing = detailsForFrom.get(toFile) ?? {};
+            const mergedLine = existing.line && normalizedLine
+                ? Math.min(existing.line, normalizedLine)
+                : (existing.line ?? normalizedLine);
+            const mergedSymbolsSet = new Set(existing.importedSymbols ?? []);
+            for (const sym of normalizedSymbols)
+                mergedSymbolsSet.add(sym);
+            const mergedSymbols = Array.from(mergedSymbolsSet);
+            detailsForFrom.set(toFile, {
+                ...(mergedLine ? { line: mergedLine } : {}),
+                ...(mergedSymbols.length > 0 ? { importedSymbols: mergedSymbols.sort() } : {})
+            });
+        }
+        // Track which symbols are imported from the target file (for unused export detection)
+        if (normalizedSymbols.length > 0) {
             if (!this.importedSymbols.has(toFile)) {
                 this.importedSymbols.set(toFile, new Set());
             }
-            for (const sym of importedSymbols) {
-                if (sym !== '*' && sym !== 'default') {
-                    this.importedSymbols.get(toFile).add(sym);
-                }
+            for (const sym of normalizedSymbols) {
+                this.importedSymbols.get(toFile).add(sym);
             }
         }
     }
@@ -642,7 +664,24 @@ export class InternalFileGraph {
         for (const [file, exps] of this.exports.entries()) {
             exports[file] = exps;
         }
-        return { imports, exports, stats: this.getStats() };
+        const importDetails = {};
+        for (const [fromFile, edges] of this.importDetails.entries()) {
+            const nested = {};
+            for (const [toFile, detail] of edges.entries()) {
+                if (!detail.line && (!detail.importedSymbols || detail.importedSymbols.length === 0))
+                    continue;
+                nested[toFile] = detail;
+            }
+            if (Object.keys(nested).length > 0) {
+                importDetails[fromFile] = nested;
+            }
+        }
+        return {
+            imports,
+            exports,
+            ...(Object.keys(importDetails).length > 0 ? { importDetails } : {}),
+            stats: this.getStats()
+        };
     }
     /**
      * Restore from JSON (for loading from .codebase-context/intelligence.json)
@@ -659,6 +698,25 @@ export class InternalFileGraph {
                 graph.exports.set(file, exps);
             }
         }
+        if (data.importDetails) {
+            for (const [fromFile, edges] of Object.entries(data.importDetails)) {
+                const edgeMap = new Map();
+                for (const [toFile, detail] of Object.entries(edges ?? {})) {
+                    edgeMap.set(toFile, detail);
+                    if (detail.importedSymbols && detail.importedSymbols.length > 0) {
+                        if (!graph.importedSymbols.has(toFile)) {
+                            graph.importedSymbols.set(toFile, new Set());
+                        }
+                        for (const sym of detail.importedSymbols) {
+                            graph.importedSymbols.get(toFile).add(sym);
+                        }
+                    }
+                }
+                if (edgeMap.size > 0) {
+                    graph.importDetails.set(fromFile, edgeMap);
+                }
+            }
+        }
         return graph;
     }
 }

package/dist/utils/usage-tracker.js.map

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package/docs/capabilities.md

@@ -1,92 +1,183 @@
-# Capabilities Reference
-
-Technical reference for what `codebase-context` ships today. For the user-facing overview, see [README.md](../README.md).
-
-## Tool Surface
-
-10 MCP tools + 1 optional resource (`codebase://context`).
-
-### Core Tools
-
-| Tool | Input | Output |
-| --- | --- | --- |
-| `search_codebase` | `query`, optional `intent`, `limit`, `filters`, `includeSnippets` | Ranked results (`file`, `summary`, `score`, `type`, `trend`, `patternWarning`) + `searchQuality` (with `hint` when low confidence) + `preflight` ({ready, reason}). Snippets opt-in. |
-| `get_team_patterns` | optional `category` | Pattern frequencies, trends, golden files, conflicts |
-| `get_component_usage` | `name` (import source) | Files importing the given package/module |
-| `remember` | `type`, `category`, `memory`, `reason` | Persists to `.codebase-context/memory.json` |
-| `get_memory` | optional `category`, `type`, `query`, `limit` | Memories with confidence decay scoring |
-
-### Utility Tools
-
-| Tool | Purpose |
-| --- | --- |
-| `get_codebase_metadata` | Framework, dependencies, project stats |
-| `get_style_guide` | Style rules from project documentation |
-| `detect_circular_dependencies` | Import cycles in the file graph |
-| `refresh_index` | Full or incremental re-index + git memory extraction |
-| `get_indexing_status` | Index state, progress, last stats |
-
-## Retrieval Pipeline
-
-Ordered by execution:
-
-1. **Intent classification** — EXACT_NAME (for symbols), CONCEPTUAL, FLOW, CONFIG, WIRING. Sets keyword/semantic weight ratio.
-2. **Query expansion** — bounded domain term expansion for conceptual queries.
-3. **Dual retrieval** — keyword (Fuse.js) + semantic (local embeddings or OpenAI).
-4. **RRF fusion** — Reciprocal Rank Fusion (k=60) across all retrieval channels.
-5. **Structure-aware boosting** — import centrality, composition root boost, path overlap, definition demotion for action queries.
-6. **Contamination control** — test file filtering for non-test queries.
-7. **File deduplication** — best chunk per file.
-8. **Stage-2 reranking** — cross-encoder (`Xenova/ms-marco-MiniLM-L-6-v2`) triggers when the score between the top files are very close. CPU-only, top-10 bounded.
-9. **Result enrichment** — compact type (`componentType:layer`), pattern momentum (`trend` Rising/Declining only, Stable omitted), `patternWarning`, condensed relationships (`importedByCount`/`hasTests`), related memories (capped to 3), search quality assessment with `hint` when low confidence.
-
-### Defaults
-
-- **Chunk size**: 50 lines, 0 overlap
-- **Reranker trigger**: activates when top-3 results are within 0.08 score of each other
-- **Embedding model**: Granite (`ibm-granite/granite-embedding-30m-english`, 8192 token context) via `@huggingface/transformers` v3
-- **Vector DB**: LanceDB with cosine distance
-
-## Preflight (Edit Intent)
-
-Returned as `preflight` when search `intent` is `edit`, `refactor`, or `migrate`. Also returned for default searches when intelligence is available.
-
-Output: `{ ready: boolean, reason?: string }`
-
-- `ready`: whether evidence is sufficient to proceed with edits
-- `reason`: when `ready` is false, explains why (e.g., "Search quality is low", "Insufficient pattern evidence")
-
-### How `ready` is determined
-
-1. **Evidence triangulation** — scores code match (45%), pattern alignment (30%), and memory support (25%). Needs combined score ≥ 40 to pass.
-2. **Epistemic stress check** — if pattern conflicts, stale memories, or thin evidence are detected, `ready` is set to false with an abstain signal.
-3. **Search quality gate** — if `searchQuality.status` is `low_confidence`, `ready` is forced to false regardless of evidence scores. This prevents the "confidently wrong" problem where evidence counts look good but retrieval quality is poor.
-
-### Internal analysis (not in output, used to compute `ready`)
-
-- Risk level from circular deps + impact breadth + failure memories
-- Preferred/avoid patterns from team pattern analysis
-- Golden files by pattern density
-- Impact candidates from import graph
-- Failure warnings from related memories
-- Pattern conflicts when two patterns in the same category are both > 20% adoption
-
-## Memory System
-
-- 4 types: `convention`, `decision`, `gotcha`, `failure`
-- Confidence decay: conventions never decay, decisions 180-day half-life, gotchas/failures 90-day half-life
-- Stale threshold: memories below 30% confidence are flagged
-- Git auto-extraction: conventional commits from last 90 days
-- Surface locations: `search_codebase` results (as `relatedMemories`), `get_team_patterns` responses, preflight analysis
-
-## Indexing
-
-- Initial: full scan → chunking (50 lines, 0 overlap) → embedding → vector DB (LanceDB) + keyword index (Fuse.js)
-- Incremental: SHA-256 manifest diffing, selective embed/delete, full intelligence regeneration
-- Auto-heal: corrupted index triggers automatic full re-index on next search
-- Storage: `.codebase-context/` directory (memory.json + generated files)
-
-## Analyzers
-
-- **Angular**: signals, standalone components, control flow syntax, lifecycle hooks, DI patterns, component metadata
-- **Generic**: 30+ languages — TypeScript, JavaScript, Python, Java, Kotlin, C/C++, C#, Go, Rust, PHP, Ruby, Swift, Scala, Shell, config/markup formats
+# Capabilities Reference
+
+Technical reference for what `codebase-context` ships today. For the user-facing overview, see [README.md](../README.md).
+
+## CLI Reference
+
+All shipped capabilities are available locally via the CLI (human-readable by default, `--json` for automation).
+For a “gallery” of commands and examples, see `docs/cli.md`.
+
+| Command | Flags | Maps to |
+|---|---|---|
+| `search --query <q>` | `--intent explore\|edit\|refactor\|migrate`, `--limit <n>`, `--lang <l>`, `--framework <f>`, `--layer <l>` | `search_codebase` |
+| `metadata` | — | `get_codebase_metadata` |
+| `status` | — | `get_indexing_status` |
+| `reindex` | `--incremental`, `--reason <r>` | equivalent to `refresh_index` |
+| `style-guide` | `--query <q>`, `--category <c>` | `get_style_guide` |
+| `patterns` | `--category all\|di\|state\|testing\|libraries` | `get_team_patterns` |
+| `refs --symbol <name>` | `--limit <n>` | `get_symbol_references` |
+| `cycles` | `--scope <path>` | `detect_circular_dependencies` |
+| `memory list` | `--category`, `--type`, `--query`, `--json` | — |
+| `memory add` | `--type`, `--category`, `--memory`, `--reason` | `remember` |
+| `memory remove <id>` | — | — |
+
+All commands accept `--json` for raw JSON output. Errors go to stderr with exit code 1.
+
+```bash
+# Quick examples
+npx codebase-context status
+npx codebase-context search --query "auth middleware" --intent edit
+npx codebase-context refs --symbol "UserService" --limit 10
+npx codebase-context cycles --scope src/features
+npx codebase-context reindex --incremental
+```
+
+## Tool Surface
+
+10 MCP tools + 1 optional resource (`codebase://context`). **Migration:** `get_component_usage` was removed; use `get_symbol_references` for symbol usage evidence.
+
+### Core Tools
+
+| Tool                    | Input                                                             | Output                                                                                                                                                                                                                  |
+| ----------------------- | ----------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `search_codebase`       | `query`, optional `intent`, `limit`, `filters`, `includeSnippets` | Ranked results (`file`, `summary`, `score`, `type`, `trend`, `patternWarning`, `relationships`, `hints`) + `searchQuality` + decision card (`ready`, `nextAction`, `patterns`, `bestExample`, `impact`, `whatWouldHelp`) when `intent="edit"`. Hints capped at 3 per category. |
+| `get_team_patterns`     | optional `category`                                               | Pattern frequencies, trends, golden files, conflicts                                                                                                                                 |
+| `get_symbol_references` | `symbol`, optional `limit`                                        | Concrete symbol usage evidence: `usageCount` + top usage snippets + `confidence` + `isComplete`. `confidence: "syntactic"` means static/source-based only (no runtime or dynamic dispatch). When Tree-sitter + file content are available, comments and string literals are excluded from the scan — the count reflects real identifier nodes only. Replaces the removed `get_component_usage`. |
+| `remember`              | `type`, `category`, `memory`, `reason`                            | Persists to `.codebase-context/memory.json`                                                                                                                                          |
+| `get_memory`            | optional `category`, `type`, `query`, `limit`                     | Memories with confidence decay scoring                                                                                                                                               |
+
+### Utility Tools
+
+| Tool                           | Purpose                                              |
+| ------------------------------ | ---------------------------------------------------- |
+| `get_codebase_metadata`        | Framework, dependencies, project stats               |
+| `get_style_guide`              | Style rules from project documentation               |
+| `detect_circular_dependencies` | Import cycles in the file graph                      |
+| `refresh_index`                | Full or incremental re-index + git memory extraction |
+| `get_indexing_status`          | Index state, progress, last stats                    |
+
+## Retrieval Pipeline
+
+Ordered by execution:
+
+1. **Intent classification** — EXACT_NAME (for symbols), CONCEPTUAL, FLOW, CONFIG, WIRING. Sets keyword/semantic weight ratio.
+2. **Query expansion** — bounded domain term expansion for conceptual queries.
+3. **Dual retrieval** — keyword (Fuse.js) + semantic (local embeddings or OpenAI).
+4. **RRF fusion** — Reciprocal Rank Fusion (k=60) across all retrieval channels.
+5. **Definition-first boost** — for EXACT_NAME intent, results matching the symbol name get +15% score boost (e.g., defining file ranks above using files).
+6. **Structure-aware boosting** — import centrality, composition root boost, path overlap, definition demotion for action queries.
+7. **Contamination control** — test file filtering for non-test queries.
+8. **File deduplication** — best chunk per file.
+9. **Symbol-level deduplication** — within each `symbolPath` group, keep only the highest-scoring chunk (prevents duplicate methods from same class clogging results).
+10. **Stage-2 reranking** — cross-encoder (`Xenova/ms-marco-MiniLM-L-6-v2`) triggers when the score between the top files are very close. CPU-only, top-10 bounded.
+11. **Result enrichment** — compact type (`componentType:layer`), pattern momentum (`trend` Rising/Declining only, Stable omitted), `patternWarning`, condensed relationships (`importedByCount`/`hasTests`), structured hints (capped callers/consumers/tests ranked by frequency), scope header for symbol-aware snippets (`// ClassName.methodName`), related memories (capped to 3), search quality assessment with `hint` when low confidence.
+
+### Defaults
+
+- **Chunk size**: 50 lines, 0 overlap
+- **Reranker trigger**: activates when top-3 results are within 0.08 score of each other
+- **Embedding model**: `Xenova/bge-small-en-v1.5` (512 token context, fast, local-first) via `@huggingface/transformers`. Override: `EMBEDDING_MODEL=onnx-community/granite-embedding-small-english-r2-ONNX` for Granite (8192 ctx, slower).
+- **Vector DB**: LanceDB with cosine distance
+
+## Decision Card (Edit Intent)
+
+Returned as `preflight` when search `intent` is `edit`, `refactor`, or `migrate`.
+
+**Output shape:**
+
+```typescript
+{
+  ready: boolean;
+  nextAction?: string;        // Only when ready=false; what to search for next
+  warnings?: string[];        // Failure memories (capped at 3)
+  patterns?: {
+    do: string[];             // Top 3 preferred patterns with adoption %
+    avoid: string[];          // Top 3 declining patterns
+  };
+  bestExample?: string;       // Top 1 golden file (path format)
+  impact?: {
+    coverage?: string;        // "X/Y callers in results"
+    files?: string[];         // Back-compat: top impact candidates (paths only)
+    details?: Array<{ file: string; line?: number; hop: 1 | 2 }>; // When available
+  };
+  whatWouldHelp?: string[];   // Concrete next steps (max 4) when ready=false
+}
+```
+
+Impact is 2-hop transitive: direct importers (hop 1) and their importers (hop 2), each labeled with distance. Capped at 20 files to avoid noise.
+
+**Fields explained:**
+
+- `ready`: boolean, whether evidence is sufficient to proceed
+- `nextAction`: actionable reason why `ready=false` (e.g., "2 of 5 callers missing")
+- `warnings`: failure memories from team (auto-surfaces past mistakes)
+- `patterns.do`: patterns the team is adopting, ranked by adoption %
+- `patterns.avoid`: declining patterns, ranked by % (useful for migrations)
+- `bestExample`: exemplar file for the area under edit
+- `impact.coverage`: shows caller visibility ("3/5 callers in results" means 2 callers weren't searched yet)
+- `impact.details`: richer impact candidates with optional `line` and hop distance (1 = direct, 2 = transitive)
+- `impact.files`: back-compat list of impact candidate paths (when details aren’t available)
+- `whatWouldHelp`: specific next searches, tool calls, or files to check that would close evidence gaps
+
+### How `ready` is determined
+
+1. **Evidence triangulation** — scores code match (45%), pattern alignment (30%), and memory support (25%). Needs combined score ≥ 40 to pass.
+2. **Epistemic stress check** — if pattern conflicts, stale memories, thin evidence, or low caller coverage are detected, `ready` is set to false.
+3. **Search quality gate** — if `searchQuality.status` is `low_confidence`, `ready` is forced to false regardless of evidence scores. This prevents the "confidently wrong" problem.
+
+### Internal signals (not in output, feed `ready` computation)
+
+- Risk level from circular deps, impact breadth, and failure memories
+- Preferred/avoid patterns from team pattern analysis
+- Golden files ranked by pattern density
+- Caller coverage from import graph (X of Y callers appearing in results)
+- Pattern conflicts when two patterns in the same category are both > 20% adoption
+- Confidence decay of related memories
+
+## Memory System
+
+- 4 types: `convention`, `decision`, `gotcha`, `failure`
+- Confidence decay: conventions never decay, decisions 180-day half-life, gotchas/failures 90-day half-life
+- Stale threshold: memories below 30% confidence are flagged
+- Git auto-extraction: conventional commits from last 90 days
+- Surface locations: `search_codebase` results (as `relatedMemories`), `get_team_patterns` responses, preflight analysis
+
+## Indexing
+
+- Initial: full scan → chunking (50 lines, 0 overlap) → embedding → vector DB (LanceDB) + keyword index (Fuse.js)
+- Incremental: SHA-256 manifest diffing, selective embed/delete, full intelligence regeneration
+- Auto-refresh (MCP server mode only): chokidar file watcher triggers incremental reindex after a debounce on any source file change — `node_modules/`, `.git/`, `dist/`, and `.codebase-context/` are excluded. One-shot CLI runs skip the watcher entirely.
+- Version gating: `index-meta.json` tracks format version; mismatches trigger automatic rebuild
+- Crash-safe rebuilds: full rebuilds write to `.staging/` and swap atomically only on success
+- Auto-heal: corrupted index triggers automatic full re-index on next search
+- Relationships sidecar: `relationships.json` contains file import graph, symbol export index, and per-edge import details (`importDetails`: line number + imported symbol names where available)
+- Storage: `.codebase-context/` directory (memory.json + generated files)
+
+## Analyzers
+
+- **Angular**: signals, standalone components, control flow syntax, lifecycle hooks, DI patterns, component metadata
+- **Generic**: 30+ have indexing/retrieval coverage including PHP, Ruby, Swift, Scala, Shell, config/markup., 10 languages have full symbol extraction (Tree-sitter: TypeScript, JavaScript, Python, Java, Kotlin, C, C++, C#, Go, Rust). 
+
+Notes:
+
+- Language detection covers common extensions including `.pyi`, `.kt`/`.kts`, `.cc`/`.cxx`, and config formats like `.toml`/`.xml`.
+- When Tree-sitter grammars are present, the Generic analyzer uses AST-aligned chunking and scope-aware prefixes for symbol-aware snippets (with fallbacks).
+
+## Evaluation Harness
+
+Reproducible evaluation is shipped as a CLI entrypoint backed by shared scoring/reporting code.
+
+- **Command:** `npm run eval -- <codebaseA> <codebaseB>` (builds first, then runs `scripts/run-eval.mjs`)
+- **Shared implementation:** `src/eval/harness.ts` + `src/eval/types.ts` (tests and CLI use the same scoring)
+- **Frozen fixtures:**
+  - `tests/fixtures/eval-angular-spotify.json` (real-world)
+  - `tests/fixtures/eval-controlled.json` + `tests/fixtures/codebases/eval-controlled/` (offline controlled)
+- **Reported metrics:** Top-1 accuracy, Top-3 recall, spec contamination rate, and a gate pass/fail
+
+## Limitations
+
+- **Symbol refs are not a call-graph.** `get_symbol_references` counts identifier-node occurrences in the AST (comments/strings excluded via Tree-sitter). It does not distinguish call sites from type annotations, variable assignments, or imports. Full call-site-specific analysis (`call_expression` nodes only) is a roadmap item.
+- **Impact is 2-hop max.** `computeImpactCandidates` walks direct importers then their importers. Full BFS reachability is on the roadmap.
+- **Angular is the only framework with a rich dedicated analyzer.** All other languages go through the Generic analyzer (30+ languages, chunking + import graph, no framework-specific signal extraction).
+- **Default embedding model is `bge-small-en-v1.5` (512-token context).** Granite (8192 context) is opt-in via `EMBEDDING_MODEL`. OpenAI is opt-in via `EMBEDDING_PROVIDER=openai` — sends code externally.
+- **Patterns are file-level frequency counts.** Not semantic clustering. Rising/Declining trend is derived from git commit recency for files using each pattern, not from usage semantics.