codestrate 0.6.2 → 0.6.3

package/README.md

@@ -1,153 +1,149 @@
-# Coding Intelligence MCP Server
+# Codestrate (coding-intelligence-mcp-server)
 
-An "external fine-tuning" layer for cloud coding models (Claude Code, Codex, Gemini, OpenCode). Provides structural code retrieval via tree-sitter AST parsing, graph-based symbol navigation, project memory, and executable validation via the Model Context Protocol.
+An "external fine-tuning" layer for cloud coding models (Claude Code, Codex, Gemini, OpenCode). Provides structural code retrieval via tree-sitter AST parsing, graph-based symbol navigation, project memory, and allowlisted validation via the Model Context Protocol.
 
 ## Architecture
 
 ```
 Model (Claude Code / Codex / OpenCode)
         │
-        │ MCP (stdio / HTTP)
+        │ MCP (stdio)
         ▼
 ┌──────────────────────────────────────────────────────┐
-│              Coding Intelligence MCP Server          │
+│              Codestrate MCP Server                   │
 ├──────────────────────────────────────────────────────┤
-│  Tools (13)                                           │
-│  ├─ ci_get_context        — [Primary] Context bundle  │
-│  ├─ ci_repo_overview      — Project structure         │
-│  ├─ ci_search_code        — Hybrid code search        │
-│  ├─ ci_inspect_symbol     — Symbol definition         │
-│  ├─ ci_search_history     — Git history               │
-│  ├─ ci_recall_experience  — Past solutions             │
-│  ├─ ci_run_validation     — Build/test/lint           │
-│  ├─ ci_record_experience  — Save knowledge            │
-│  ├─ ci_trace_flow         — BFS call/import traversal  │
-│  ├─ ci_analyze_impact     — Change impact analysis     │
-│  ├─ ci_status             — Index state report         │
-│  ├─ ci_reindex            — Rebuild symbol index       │
-│  └─ ci_explore            — AST + graph unified query  │
-│                                                         │
-│  Prompts (3)                                            │
-│  ├─ debug-runtime-error   — 10-step debug workflow     │
-│  ├─ implement-feature     — 8-step impl workflow       │
-│  └─ review-code           — 6-step review              │
+│  Profile: core (default, ≤7 tools)                   │
+│  ├─ ci_status           — Index readiness + counts   │
+│  ├─ ci_repo_overview    — Project structure          │
+│  ├─ ci_explore          — FTS5 + camelCase search    │
+│  ├─ ci_inspect_symbol   — Definition + callers       │
+│  ├─ ci_get_context      — Task context bundle        │
+│  ├─ ci_analyze_impact   — Change impact              │
+│  └─ ci_trace_flow       — Call/import BFS            │
+│                                                      │
+│  Profile: full (opt-in)                              │
+│  ├─ validation, reindex, memory, session, graph ops  │
+│  └─ set CI_MCP_PROFILE=full or "profile":"full"      │
+│                                                      │
+│  Store: SQLite only (single source of truth)         │
+│  Transport: stdio                                    │
 └──────────────────────────────────────────────────────┘
 ```
 
 ## Quick Start
 
 ```bash
-npx coding-intelligence-mcp-server
-```
-
-Or from source:
+# From package
+npx codestrate
+# or
+npx ci-mcp
 
-```bash
+# From source
 git clone <repo> && cd coding-intelligence-mcp-server
 npm install
 npm run build
 node dist/index.js
 ```
 
-## Tools
-
-### Primary Tool
-- **`ci_get_context`** — Call FIRST for any task. Takes a natural language task description and returns relevant symbols, files, tests, git history, and past experiences within a token budget.
-
-### AST & Graph Intelligence
-- **`ci_explore`** — Unified code exploration: search by FTS5 full-text, camelCase segments, or symbol name across the graph index. Returns ranked nodes + edges with neighbor context.
-- **`ci_trace_flow`** — BFS traversal of call/import graph. Given a symbol, find callers and callees up to configurable depth. Uses tree-sitter parsed AST relations.
-- **`ci_inspect_symbol`** — Symbol definition with ±5 lines context, callers, callees, related tests, and graph neighbors.
-
-### Code Intelligence
-- **`ci_repo_overview`** — Scan repository to infer structure, build system, frameworks, entry points, and commands.
-- **`ci_search_code`** — Hybrid search (ripgrep + symbol matching) with BM25 scoring, language/scope filters.
-
-### Change Analysis
-- **`ci_analyze_impact`** — Given file changes, find dependents, imports, exports, and related tests using the graph index.
-- **`ci_status`** — Report index state: repo fingerprint, commit, indexed age, symbol/relation counts, staleness detection.
-- **`ci_reindex`** — Rebuild the symbol index from scratch (full) or via git diff (incremental).
-
-### Memory & Learning
-- **`ci_recall_experience`** — Retrieve past verified fixes and knowledge (hybrid: experiences + semantic memories).
-- **`ci_record_experience`** — Save a verified bug-fix with validation evidence (commit SHA, changed files, build/test pass).
-
-### Validation
-- **`ci_run_validation`** — Execute build/test/lint from config allowlist (permission-gated).
+Default **profile is `core`** (read-only, ≤7 tools). Mutations and extra diagnostics require full:
 
-### Git
-- **`ci_search_history`** — Search git commit history by message query.
-
-## Configuration
+```bash
+CI_MCP_PROFILE=full node dist/index.js
+```
 
-Create `.ci-mcp.json` in your project root:
+Or in `.ci-mcp.json`:
 
 ```json
 {
+  "profile": "full",
   "commands": {
     "build": "npm run build",
     "test": "npm test",
     "lint": "npm run lint"
   },
+  "validation": { "trusted": true },
   "timeout": 300,
   "storePath": "~/.ci-mcp/store"
 }
 ```
 
-Transport modes:
-- `stdio` (default) — for local use with Claude Code, OpenCode
-- `TRANSPORT=http PORT=3000` — for remote/HTTP access
+### Semantic search (automatic by default)
+
+On first start, codestrate **auto-downloads** LFM2.5-Embedding GGUF + `llama-server`, **spawns** a local embeddings process, indexes vectors, and uses **hybrid** search when ready.
+
+Artifacts live under `~/.ci-mcp/` (`models/`, `bin/`, `store/`). Disable with `CI_MCP_EMBEDDING_MODE=none`.
+
+Full guide: [`docs/semantic-search.md`](docs/semantic-search.md).
+
+## Tools
+
+### Core (default)
+
+| Tool | Purpose |
+|------|---------|
+| `ci_status` | Index lifecycle, readiness, symbol counts, staleness |
+| `ci_repo_overview` | Structure, build system, frameworks, entry points |
+| `ci_explore` | FTS5 + camelCase + graph search |
+| `ci_inspect_symbol` | Definition, callers, callees, tests |
+| `ci_get_context` | Token-budgeted context bundle for a task |
+| `ci_analyze_impact` | Dependents / symbols affected by file changes |
+| `ci_trace_flow` | BFS call/import flow |
+
+### Full profile only
+
+- `ci_search_code`, `ci_search_history`, `ci_deep_explore`
+- Graph: `ci_graph_stats`, `ci_graph_explain`, `ci_query_graph`, `ci_detect_cycles`, `ci_trace_bfs`, `ci_detect_dead_code`
+- Memory: `ci_recall_experience`, `ci_record_experience` (evidence-gated)
+- Validation: `ci_run_validation` (requires `validation.trusted: true`)
+- Index: `ci_reindex`
+- Session: `ci_session_heartbeat`, `ci_session_status`, `ci_reflect`, `ci_reflect_history`
+- Meta: `ci_profile`, `ci_ping`
 
 ## Features
 
-### Tree-Sitter AST Parsing
-TypeScript and Python files are parsed via WASM-compiled tree-sitter grammars. The parser extracts:
-- Symbol definitions (class, interface, function, method, type, enum, variable)
-- Call relationships (who calls whom)
-- Import statements (dependency edges)
-- Export declarations
-
-Two WASM grammars (~1.8 MB total) ship with the npm package and load lazily.
-
-### Graph Model
-A directed graph of symbol dependencies is stored in SQLite with FTS5 full-text search:
-- **Nodes**: each symbol (class, function, method, etc.) is a node
-- **Edges**: calls, extends, implements, imports, composes — all stored as typed edges
-- **Search**: FTS5 (BM25-ranked), LIKE fallback, and **camelCase-aware** matching (`getUserData` → matches `%get%User%Data%`)
-- **Traversal**: BFS shortest-path search on the edge graph
-
-### SQLite Store (Production)
-The default persistence backend uses `better-sqlite3` with:
-- Schema migrations (5 current — initial, experiences, memories, FTS5, graph)
-- WAL journal for concurrent reads
-- Foreign key cascading for graph edge cleanup
-- In-memory mode available for tests
-
-## Comparison to Xanther
-
-| Feature | Xanther XCE | This Server |
-|---------|-------------|-------------|
-| Backend | Hosted | **Local/self-host** |
-| Symbol index | ✅ PRAT | **✅ Tree-sitter AST** |
-| Symbol graph | ❌ | **✅ BFS + FTS5 + camelCase** |
-| Code search | ✅ Semantic | ✅ Hybrid (rg + symbol) |
-| Context bundle | ✅ xce_get_context | ✅ ci_get_context |
-| Execution | ❌ | **✅ Build/test/lint** |
-| Verified memory | ❌ (XME Coming Soon) | **✅ Quality-scored** |
-| Steering files | ✅ | ✅ Prompts included |
-| Open source | Integration only | **Full code** |
+### Tree-sitter AST + graph
+
+Bundled WASM grammars (TypeScript, TSX, JavaScript, Python, Go, Rust, Java, C, C++). Symbols and relations land in **SQLite** with FTS5 and camelCase matching. Graph BFS powers `ci_trace_flow` / impact tools.
+
+### Index readiness
+
+Auto-index runs on startup when `repoPath` is known. Lifecycle states: `not_started` | `indexing` | `ready` | `failed` | `empty`. Failed indexes **do not** report ready; tools that need the graph return typed `INDEX_FAILED` / `INDEX_NOT_READY` errors instead of empty success.
+
+### Evidence-gated memory
+
+`ci_record_experience` (full profile) requires commit SHA, changed files, and validation evidence before storing.
+
+### Validation trust
+
+`ci_run_validation` is default-off. Enable only after reviewing allowlisted commands and setting `"validation": { "trusted": true }`.
+
+## Configuration
+
+Config files (first found wins): `.ci-mcp.json`, `ci-mcp.config.json`, `.coding-intelligence.json`.
+
+| Key | Default | Notes |
+|-----|---------|-------|
+| `profile` | `core` | or env `CI_MCP_PROFILE=full` |
+| `storePath` | `~/.ci-mcp/store` | SQLite DB location |
+| `commands.*` | — | build/test/lint allowlist |
+| `validation.trusted` | `false` | must be true to run validation |
+| `timeout` | `300` | seconds |
+
+## Transport
+
+**stdio only.** Streamable HTTP is not shipped in this version.
 
 ## Prompts
 
-Accessible as MCP Prompt resources:
 - `ci://prompts/debug-runtime-error`
 - `ci://prompts/implement-feature`
 - `ci://prompts/review-code`
 
 ## Limitations
-- C++/Rust/Go/PHP AST parsing not yet available (only tree-sitter typescript + python WASM grammars are bundled)
-- JSON store (default) doesn't support FTS5 — SQLite mode required for full-text search
-- Incremental reindex (`ci_reindex --mode incremental`) uses git diff but only covers changed files, not cascading dependents
+
+- Relation resolution is still partly name-based (heuristic edges may be wrong for overloads)
+- Incremental reindex improves over full rebuild but cascading dependents are best-effort
+- Regex fallback languages are best-effort vs tree-sitter grammars
 
 ## License
 

package/dist/constants.d.ts

@@ -1,6 +1,6 @@
 import { type CIConfig } from "./types.js";
 export declare const SERVER_NAME = "coding-intelligence-mcp-server";
-export declare const SERVER_VERSION = "0.6.1";
+export declare const SERVER_VERSION = "0.6.2";
 export declare const DEFAULT_STORE_PATH: string;
 export declare const INDEX_FILE = "index.json";
 export declare const MEMORY_FILE = "memory.json";

package/dist/constants.d.ts.map

@@ -1 +1 @@
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package/dist/constants.js

@@ -3,7 +3,7 @@ import { join, resolve } from "path";
 import { existsSync, readFileSync } from "fs";
 // ─── Server identity ──────────────────────────────────────
 export const SERVER_NAME = "coding-intelligence-mcp-server";
-export const SERVER_VERSION = "0.6.1";
+export const SERVER_VERSION = "0.6.2";
 // ─── Default paths ────────────────────────────────────────
 export const DEFAULT_STORE_PATH = join(homedir(), ".ci-mcp", "store");
 export const INDEX_FILE = "index.json";
@@ -113,17 +113,25 @@ export function loadConfig(repoPath) {
                     repoPath: basePath,
                     storePath: cfg.storePath || DEFAULT_STORE_PATH,
                     maxResponseChars: cfg.maxResponseChars || MAX_RESPONSE_CHARS,
+                    profile: process.env.CI_MCP_PROFILE === "full" ? "full" : (cfg.profile === "full" ? "full" : "core"),
                     validation: {
                         commands: {
                             build: cfg.commands?.build ?? null,
                             test: cfg.commands?.test ?? null,
                             lint: cfg.commands?.lint ?? null,
                         },
+                        trusted: cfg.validation?.trusted === true,
+                        trustedRoot: cfg.validation?.trustedRoot,
+                        trustedFingerprint: cfg.validation?.trustedFingerprint,
                         timeout: cfg.timeout ?? DEFAULT_VALIDATION_TIMEOUT,
                         maxOutput: cfg.maxOutput ?? MAX_VALIDATION_OUTPUT,
                     },
-                    embeddingMode: cfg.embeddingMode || "none",
-                    embeddingApi: cfg.embeddingApi,
+                    embeddingMode: parseEmbeddingMode(cfg.embeddingMode),
+                    embeddingApi: normalizeEmbeddingApi(cfg.embeddingApi),
+                    embeddingDim: typeof cfg.embeddingDim === "number" && cfg.embeddingDim > 0
+                        ? cfg.embeddingDim
+                        : 1024,
+                    vectorStore: parseVectorStore(cfg.vectorStore, cfg.embeddingMode),
                 };
             }
             catch {
@@ -136,12 +144,54 @@ export function loadConfig(repoPath) {
         repoPath: basePath,
         storePath: DEFAULT_STORE_PATH,
         maxResponseChars: MAX_RESPONSE_CHARS,
+        profile: process.env.CI_MCP_PROFILE === "full" ? "full" : "core",
         validation: {
             commands: { build: undefined, test: undefined, lint: undefined },
+            trusted: false,
             timeout: DEFAULT_VALIDATION_TIMEOUT,
             maxOutput: MAX_VALIDATION_OUTPUT,
         },
-        embeddingMode: "none",
+        embeddingMode: parseEmbeddingMode(undefined),
+        embeddingDim: 1024,
+        vectorStore: parseVectorStore(undefined, "auto"),
+    };
+}
+function parseEmbeddingMode(raw) {
+    const env = process.env.CI_MCP_EMBEDDING_MODE?.trim().toLowerCase();
+    if (env === "none" || env === "0" || env === "off" || env === "false") {
+        return "none";
+    }
+    if (env === "auto" || env === "api" || env === "subprocess")
+        return env;
+    if (process.env.CI_MCP_AUTO_EMBED === "0")
+        return "none";
+    if (raw === "api" || raw === "subprocess" || raw === "none" || raw === "auto") {
+        return raw;
+    }
+    // Default: fully automatic local runtime
+    return "auto";
+}
+function parseVectorStore(raw, embeddingMode) {
+    if (raw === "none" || raw === "zvec" || raw === "memory")
+        return raw;
+    // When embedding is on and vectorStore omitted → default zvec
+    if (embeddingMode === "api" ||
+        embeddingMode === "subprocess" ||
+        embeddingMode === "auto" ||
+        embeddingMode === undefined) {
+        return "zvec";
+    }
+    return "none";
+}
+function normalizeEmbeddingApi(raw) {
+    if (!raw || typeof raw !== "object")
+        return undefined;
+    const o = raw;
+    const url = typeof o.url === "string" ? o.url : "http://127.0.0.1:18765";
+    return {
+        url,
+        model: typeof o.model === "string" ? o.model : undefined,
+        apiKey: typeof o.apiKey === "string" ? o.apiKey : undefined,
     };
 }
 //# sourceMappingURL=constants.js.map

package/dist/constants.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -1,4 +1,5 @@
 #!/usr/bin/env node
-/** True once auto-reindex has completed at least once. */
-export declare function isIndexReady(): boolean;
+import { isIndexReady } from "./services/index-state.js";
+/** @deprecated Prefer isIndexReady from index-state — kept for external importers. */
+export { isIndexReady };
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAoBA,OAAO,EAML,YAAY,EACb,MAAM,2BAA2B,CAAC;AAkDnC,sFAAsF;AACtF,OAAO,EAAE,YAAY,EAAE,CAAC"}