npm - ai-spector - Versions diffs - 0.8.0 → 0.8.2 - Mend

ai-spector 0.8.0 → 0.8.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (19) hide show

package/dist/cli.js +2 -2
package/dist/cli.js.map +1 -1
package/dist/core/operations/cocoindex.d.ts +0 -7
package/dist/core/operations/cocoindex.d.ts.map +1 -1
package/dist/core/operations/cocoindex.js +5 -10
package/dist/core/operations/cocoindex.js.map +1 -1
package/package.json +1 -1
package/scaffold/claude/CLAUDE.md +53 -30
package/scaffold/cocoindex/flow.py +127 -80
package/scaffold/cocoindex/pipeline.py +33 -5
package/scaffold/cocoindex/pyproject.toml +2 -3
package/scaffold/cocoindex/requirements.txt +5 -6
package/scaffold/cocoindex/server.py +113 -13
package/scaffold/cursor/skills/ai-spector/SKILL.md +16 -1
package/scaffold/cursor/skills/ai-spector-graph/SKILL.md +1 -1
package/scaffold/cursor/skills/ai-spector-graph/references/analyze.md +16 -7
package/scaffold/cursor/skills/ai-spector-graph/references/impact.md +20 -16
package/scaffold/cursor/skills/ai-spector-graph/references/index.md +17 -26
package/scaffold/cursor/skills/ai-spector-graph/references/validate-graph.md +10 -2

package/dist/cli.js CHANGED Viewed

@@ -676,7 +676,7 @@ cocoindex
     .description("Run the CocoIndex pipeline to update embeddings (requires Python)")
     .option("--root <path>", "Project root (default: cwd)")
     .action(async (opts) => {
-    const { resolve: res } = await import("node:path");
+    const { resolve: res, join } = await import("node:path");
     const { isCocoindexConfigured, cocoindexPipelinePath, cocoindexDir, findPython } = await import("./core/operations/cocoindex.js");
     const root = res(opts.root ?? process.cwd());
     if (!(await isCocoindexConfigured(root))) {
@@ -696,7 +696,7 @@ cocoindex
     }
     const { spawn } = await import("node:child_process");
     await new Promise((resolveP, reject) => {
-        const child = spawn(pythonBin, [pipelinePath, "update"], {
+        const child = spawn(pythonBin, [join(cocoindexDir(root), "pipeline.py"), "update"], {
             cwd: root,
             stdio: "inherit",
             env: { ...process.env, AI_SPECTOR_ROOT: root },

package/dist/cli.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/core/operations/cocoindex.d.ts CHANGED Viewed

@@ -5,13 +5,6 @@ export type CocoindexInstallMode = "venv" | "global";
 export declare function findPython(cocoDir: string): Promise<string>;
 /** Returns [command, ...args] for running pipeline.py in MCP mode.
  *  Priority: uv (inline deps, no venv required) → venv python → python3 → python */
-/** Returns the command for running server.py in MCP mode.
- *  Always uses the venv python so startup is instant — no downloads.
- *  Deps must be pre-installed via runCocoindexSetup before calling this. */
-export declare function buildMcpCommand(cocoDir: string, _pipelinePath: string): Promise<{
-    command: string;
-    args: string[];
-}>;
 /** Check python version is ≥3.11. Returns version string or null on failure. */
 export declare function checkPythonVersion(bin: string): Promise<string | null>;
 export declare function cocoindexDir(root: string): string;

package/dist/core/operations/cocoindex.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/core/operations/cocoindex.js CHANGED Viewed

@@ -32,14 +32,6 @@ export async function findPython(cocoDir) {
 }
 /** Returns [command, ...args] for running pipeline.py in MCP mode.
  *  Priority: uv (inline deps, no venv required) → venv python → python3 → python */
-/** Returns the command for running server.py in MCP mode.
- *  Always uses the venv python so startup is instant — no downloads.
- *  Deps must be pre-installed via runCocoindexSetup before calling this. */
-export async function buildMcpCommand(cocoDir, _pipelinePath) {
-    const serverPath = join(cocoDir, "server.py");
-    const pythonBin = await findPython(cocoDir);
-    return { command: pythonBin, args: [serverPath] };
-}
 /** Check python version is ≥3.11. Returns version string or null on failure. */
 export async function checkPythonVersion(bin) {
     try {
@@ -178,8 +170,11 @@ export async function runCocoindexSetup(opts = {}) {
 /** Merge the cocoindex MCP server entry into <root>/.mcp.json */
 async function writeCocoindexMcpEntry(root, pipelinePath, cocoDir) {
     const { writeJson } = await import("../util/fs.js");
-    const { command, args } = await buildMcpCommand(cocoDir, pipelinePath);
-    const entry = { command, args, env: { AI_SPECTOR_ROOT: root } };
+    const entry = {
+        command: await findPython(cocoDir),
+        args: [join(cocoDir, "server.py")],
+        env: { AI_SPECTOR_ROOT: root },
+    };
     // Write to all MCP config files that exist or should be created
     const mcpFiles = [
         join(root, ".mcp.json"), // Claude Code

package/dist/core/operations/cocoindex.js.map CHANGED Viewed

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "ai-spector",
-  "version": "0.8.0",
+  "version": "0.8.2",
   "description": "Cursor-first documentation workflow: traceability graph, SRS/basic/detail design templates, and ai-spector CLI",
   "type": "module",
   "license": "MIT",

package/scaffold/claude/CLAUDE.md CHANGED Viewed

@@ -1,51 +1,64 @@
 # AI Spector — Claude Agent Rules
-You are working in an **AI Spector** managed project. The agent workflow is: read skills, run `npx ai-spector` CLI, report results. You do not write doc content from scratch — CLI + skills do the work.
+You are working in an **AI Spector** managed project. The agent workflow is: read skills, call **MCP tools** (preferred) or `npx ai-spector` CLI (fallback), report results. You do not write doc content from scratch — MCP tools / CLI + skills do the work.
 Enable all skills under `.claude/skills/` before starting.
 ## Mandatory Rules
-### 1. Refresh index before any staleness check
+### 1. MCP first, CLI fallback
+When the `ai-spector` MCP server is available, **call the MCP tool** instead of shelling out to `npx ai-spector`.
+| Operation | MCP tool | CLI fallback |
+|-----------|----------|--------------|
+| Re-index project | `index({})` | `npx ai-spector index` |
+| Merge knowledge → graph | `graph_merge({ fromKnowledge: true })` | `npx ai-spector graph merge --from-knowledge` |
+| Validate graph | `graph_validate({})` | `npx ai-spector graph validate` |
+| Impact analysis | `graph_impact({ originId, change })` | `npx ai-spector graph impact …` |
+| Walk graph from node | `graph_query({ id })` | `npx ai-spector graph query <id> --json` |
+| **Analyze data-source** | *(CLI only — no MCP tool)* | `npx ai-spector analyze` |
+### 2. Refresh index before any staleness check
 Before checking translation status, pending queue, or "what's outdated":
-```bash
-npx ai-spector index
+```
+index({})                    # MCP preferred
+npx ai-spector index         # CLI fallback
 ```
 Then read the queue. **Never read `.ai-spector/.docflow/translation-queue/pending.json` without running index first** — the queue is only accurate after indexing.
-### 2. Check impact before finishing any doc edit
+### 3. Check impact before finishing any doc edit
 After editing any file under `docs/srs/`, `docs/basic-design/`, or `docs/detail-design/`, run impact before closing the task:
-```bash
-npx ai-spector graph impact --git --change content_change --json
+```
+graph_impact({ git: true, change: "content_change" })   # MCP preferred
+npx ai-spector graph impact --git --change content_change --json  # CLI fallback
 ```
-Then run index to refresh the translation queue:
+Then refresh index:
-```bash
-npx ai-spector index
+```
+index({})
 ```
 Skip only when the user explicitly says it was a typo-only fix with no traceability concern.
-### 3. Use CLI and graph — not file search
-When you need to find, query, or understand the project graph:
+### 4. Use MCP/graph — not file search
-| Need | Use |
-|------|-----|
-| Find what needs regeneration | `npx ai-spector graph impact` |
-| Find doc/section/node by exact ID | `npx ai-spector graph query <id> --json` |
-| Find doc/section/node by concept | `graph_query_fuzzy(query: "…")` (MCP) — requires CocoIndex |
-| Search docs by meaning | `docs_search(query: "…")` (MCP) — requires CocoIndex |
-| Check graph health | `npx ai-spector graph validate` |
-| See pending translations | `npx ai-spector lang queue pending --json` (after index) |
+| Need | MCP (preferred) | CLI fallback |
+|------|-----------------|--------------|
+| Find what needs regeneration | `graph_impact({ git: true, change: "content_change" })` | `npx ai-spector graph impact --git --json` |
+| Find node by exact ID | `graph_query({ id: "…" })` | `npx ai-spector graph query <id> --json` |
+| Find node by concept | `graph_query_fuzzy(query: "…")` — requires CocoIndex | — |
+| Search docs by meaning | `docs_search(query: "…")` — requires CocoIndex | — |
+| Check graph health | `graph_validate({})` | `npx ai-spector graph validate` |
+| See pending translations | *(CLI only)* | `npx ai-spector lang queue pending --json` (after index) |
-**Only fall back to `grep` or `Read` when the CLI returns no results or you need raw file content for editing.**
+**Only fall back to `grep` or `Read` when the tool returns no results or you need raw file content for editing.**
 ## Skill → task mapping
@@ -64,13 +77,25 @@ When you need to find, query, or understand the project graph:
 | Resolve translations | `ai-spector-resolve-translation` |
 | Resolve comments | `ai-spector-resolve-comments` |
-## CLI quick reference
+## Quick reference
+### MCP tools (prefer these)
+| Tool | Purpose |
+|------|---------|
+| `index({})` | Refresh fingerprints + translation queue |
+| `graph_merge({ fromKnowledge: true })` | Merge knowledge.json into graph |
+| `graph_validate({})` | Check graph integrity |
+| `graph_impact({ git: true, change: "content_change" })` | Impact of current git diff |
+| `graph_query({ id: "…" })` | Walk graph from a node |
+### CLI (fallback / MCP-unavailable or no tool equivalent)
 ```bash
-npx ai-spector analyze              # ingest data-source, build graph
-npx ai-spector index                # refresh fingerprints + translation queue
-npx ai-spector graph validate       # check graph integrity
-npx ai-spector graph impact --git --json   # impact of current git diff (+ semantic suggestions if CocoIndex configured)
+npx ai-spector analyze              # ingest data-source, build graph (no MCP equivalent)
+npx ai-spector index                # fallback for index({})
+npx ai-spector graph validate       # fallback for graph_validate({})
+npx ai-spector graph impact --git --json   # fallback for graph_impact({ git: true })
 npx ai-spector lang queue pending --json   # pending translation jobs
 npx ai-spector setup --check        # audit project setup
 npx ai-spector template list        # list installed packs + active
@@ -81,11 +106,9 @@ npx ai-spector template use <name>  # switch active pack (use "builtin" to rever
 # CocoIndex (opt-in — requires Python 3.11+)
 npx ai-spector cocoindex setup      # scaffold pipeline into project
 npx ai-spector cocoindex index      # run pipeline (update embeddings)
-npx ai-spector cocoindex search --query "login flow"   # semantic search
-npx ai-spector cocoindex query-fuzzy --query "login"   # natural language → graph node + subgraph
 ```
-On CLI failure: show the output, offer fix / workaround / pause. Do not invent results.
+On MCP tool or CLI failure: show the output, offer fix / workaround / pause. Do not invent results.
 ## Pipeline order

package/scaffold/cocoindex/flow.py CHANGED Viewed

@@ -1,105 +1,152 @@
 """
-CocoIndex flow definition and shared search logic for ai-spector.
+CocoIndex 1.0 flow definition and search logic for ai-spector.
-Config is read from environment variables:
+Config via environment variables:
   AI_SPECTOR_ROOT       — project root (default: cwd)
-  COCOINDEX_DB_URL      — Postgres URL; omit to use LanceDB
+  COCOINDEX_DB_URI      — LanceDB URI (default: <cocoindex_dir>/lancedb_data)
   COCOINDEX_EMBED_MODEL — embedding model (default: all-MiniLM-L6-v2)
-                          prefix with "openai:" to use OpenAI embeddings
 """
+from __future__ import annotations
 import json
 import os
-import sys
+from dataclasses import dataclass
 from pathlib import Path
+from typing import Annotated, AsyncIterator
+from numpy.typing import NDArray
-import cocoindex
+import cocoindex as coco
+from cocoindex.connectors import lancedb, localfs
+from cocoindex.ops.text import RecursiveSplitter
+from cocoindex.ops.sentence_transformers import SentenceTransformerEmbedder
+from cocoindex.resources.chunk import Chunk
+from cocoindex.resources.file import FileLike, PatternFilePathMatcher
+from cocoindex.resources.id import IdGenerator
+# ── Config ────────────────────────────────────────────────────────────────────
+_SCRIPT_DIR = Path(__file__).parent
 PROJECT_ROOT = Path(os.getenv("AI_SPECTOR_ROOT", str(Path.cwd())))
 INDEX_CONFIG = PROJECT_ROOT / ".ai-spector/.docflow/config/index.docs.json"
-LANCE_PATH = str(PROJECT_ROOT / ".ai-spector/.docflow/cocoindex/lance_data")
-DB_URL = os.getenv("COCOINDEX_DB_URL", "")
+LANCEDB_URI = os.getenv(
+    "COCOINDEX_DB_URI",
+    str(_SCRIPT_DIR / "lancedb_data"),
+)
+TABLE_NAME = "doc_chunks"
 EMBED_MODEL = os.getenv(
     "COCOINDEX_EMBED_MODEL",
     "sentence-transformers/all-MiniLM-L6-v2",
 )
-def load_doc_roots() -> list[str]:
-    if not INDEX_CONFIG.exists():
-        raise FileNotFoundError(
-            f"index.docs.json not found at {INDEX_CONFIG}\n"
-            "Run `npx ai-spector index` first to create it."
-        )
-    cfg = json.loads(INDEX_CONFIG.read_text())
-    roots = []
-    for src in cfg.get("sources", {}).values():
-        p = PROJECT_ROOT / src["root"]
-        if p.exists():
-            roots.append(str(p))
+# ── Context keys ──────────────────────────────────────────────────────────────
+LANCE_DB = coco.ContextKey[lancedb.LanceAsyncConnection]("ai_spector_db")
+EMBEDDER = coco.ContextKey[SentenceTransformerEmbedder]("embedder", detect_change=True)
+_splitter = RecursiveSplitter()
+# ── Schema ────────────────────────────────────────────────────────────────────
+@dataclass
+class DocChunk:
+    id: int
+    filename: str
+    heading: str
+    chunk_start: int
+    chunk_end: int
+    text: str
+    embedding: Annotated[NDArray, EMBEDDER]
+# ── Lifespan ──────────────────────────────────────────────────────────────────
+@coco.lifespan
+async def coco_lifespan(builder: coco.EnvironmentBuilder) -> AsyncIterator[None]:
+    conn = await lancedb.connect_async(LANCEDB_URI)
+    builder.provide(LANCE_DB, conn)
+    builder.provide(EMBEDDER, SentenceTransformerEmbedder(EMBED_MODEL))
+    yield
+# ── Pipeline ──────────────────────────────────────────────────────────────────
+def _extract_heading(text: str) -> str:
+    """Return first markdown heading found, or empty string."""
+    for line in text.splitlines():
+        if line.startswith("#"):
+            return line.lstrip("#").strip()
+    return ""
+@coco.fn
+async def process_chunk(
+    chunk: Chunk,
+    filename: str,
+    id_gen: IdGenerator,
+    table: lancedb.TableTarget[DocChunk],
+) -> None:
+    table.declare_row(
+        row=DocChunk(
+            id=await id_gen.next_id(chunk.text),
+            filename=filename,
+            heading=_extract_heading(chunk.text),
+            chunk_start=chunk.start.char_offset,
+            chunk_end=chunk.end.char_offset,
+            text=chunk.text,
+            embedding=await coco.use_context(EMBEDDER).embed(chunk.text),
+        ),
+    )
+@coco.fn(memo=True)
+async def process_file(
+    file: FileLike,
+    table: lancedb.TableTarget[DocChunk],
+) -> None:
+    text = await file.read_text()
+    chunks = _splitter.split(
+        text, chunk_size=400, chunk_overlap=50, language="markdown"
+    )
+    id_gen = IdGenerator()
+    await coco.map(process_chunk, chunks, str(file.file_path.path), id_gen, table)
+def _load_doc_roots() -> list[Path]:
+    roots: list[Path] = []
+    if INDEX_CONFIG.exists():
+        cfg = json.loads(INDEX_CONFIG.read_text())
+        for src in cfg.get("sources", {}).values():
+            p = PROJECT_ROOT / src["root"]
+            if p.exists():
+                roots.append(p)
     data_source = PROJECT_ROOT / "docs" / "data-source"
     if data_source.exists():
-        roots.append(str(data_source))
+        roots.append(data_source)
     return roots
-def make_embed():
-    if EMBED_MODEL.startswith("openai:"):
-        return cocoindex.functions.OpenAIEmbed(model=EMBED_MODEL.removeprefix("openai:"))
-    return cocoindex.functions.SentenceTransformerEmbed(model=EMBED_MODEL)
-def make_storage():
-    if DB_URL:
-        return cocoindex.storages.Postgres(table_name="doc_chunks")
-    return cocoindex.storages.LanceDB(uri=LANCE_PATH, table_name="doc_chunks")
+@coco.fn
+async def app_main() -> None:
+    target_table = await lancedb.mount_table_target(
+        LANCE_DB,
+        table_name=TABLE_NAME,
+        table_schema=await lancedb.TableSchema.from_class(
+            DocChunk, primary_key=["id"]
+        ),
+    )
+    for root in _load_doc_roots():
+        files = localfs.walk_dir(
+            root,
+            recursive=True,
+            path_matcher=PatternFilePathMatcher(included_patterns=["**/*.md"]),
+        )
+        await coco.mount_each(process_file, files.items(), target_table)
-@cocoindex.flow_def(name="ai_spector_docs")
-def docs_flow(flow_builder: cocoindex.FlowBuilder, db: cocoindex.DataScope):
-    embed = make_embed()
-    storage = make_storage()
-    for root in load_doc_roots():
-        docs = flow_builder.add_source(
-            cocoindex.sources.LocalFile(
-                path=root,
-                included_patterns=["**/*.md"],
-            )
-        )
-        chunks = docs.transform(
-            cocoindex.functions.SplitRecursively(),
-            language="markdown",
-            chunk_size=400,
-            chunk_overlap=50,
-        )
-        chunks.transform(embed).save_to(db["doc_chunks"], storage)
-def search(query: str, limit: int = 5, threshold: float = 0.75) -> list[dict]:
-    """Returns a list of result dicts; never raises (errors return [])."""
-    try:
-        query_vec = make_embed().embed_query(query)
-    except Exception as e:
-        sys.stderr.write(f"Embedding failed: {e}\n")
-        return []
-    try:
-        rows = make_storage().search(
-            table="doc_chunks",
-            vector=query_vec,
-            limit=limit,
-            score_threshold=threshold,
-        )
-    except Exception as e:
-        sys.stderr.write(f"Search failed: {e}\n")
-        return []
-    return [
-        {
-            "docPath": row.get("filename", ""),
-            "heading": row.get("heading", ""),
-            "excerpt": row.get("text", ""),
-            "score": round(float(row.get("score", 0)), 4),
-        }
-        for row in rows
-    ]
+app = coco.App(
+    coco.AppConfig(name="ai_spector_docs"),
+    app_main,
+)

package/scaffold/cocoindex/pipeline.py CHANGED Viewed

@@ -6,13 +6,38 @@ ai-spector CocoIndex — CLI entry point.
   python pipeline.py search --query X Semantic search (used by ai-spector Node CLI)
 """
+from __future__ import annotations
+import asyncio
 import json
 import os
 import sys
-import cocoindex
+from flow import EMBED_MODEL, LANCEDB_URI, TABLE_NAME, app
-from flow import search
+async def _search(query: str, limit: int, threshold: float) -> list[dict]:
+    from cocoindex.connectors import lancedb
+    from cocoindex.ops.sentence_transformers import SentenceTransformerEmbedder
+    try:
+        embedder = SentenceTransformerEmbedder(EMBED_MODEL)
+        query_vec = await embedder.embed(query)
+        conn = await lancedb.connect_async(LANCEDB_URI)
+        table = await conn.open_table(TABLE_NAME)
+        results = await (await table.search(query_vec, vector_column_name="embedding")).limit(limit).to_list()
+        return [
+            {
+                "docPath": r["filename"],
+                "heading": r.get("heading", ""),
+                "excerpt": r["text"],
+                "score": round(float(1.0 - r.get("_distance", 1.0)), 4),
+            }
+            for r in results
+            if (1.0 - r.get("_distance", 1.0)) >= threshold
+        ]
+    except Exception as e:
+        sys.stderr.write(f"Search failed: {e}\n")
+        return []
 if __name__ == "__main__":
@@ -33,10 +58,13 @@ if __name__ == "__main__":
             default=float(os.getenv("COCOINDEX_SIMILARITY_THRESHOLD", "0.75")),
         )
         args = parser.parse_args(sys.argv[2:])
-        print(json.dumps(search(args.query, args.limit, args.threshold)))
+        print(json.dumps(asyncio.run(_search(args.query, args.limit, args.threshold))))
     elif cmd == "update":
-        cocoindex.cli.cli(["update", "--app", "flow.py"], standalone_mode=True)
+        app.update_blocking(report_to_stdout=True)
     else:
-        cocoindex.cli.cli(standalone_mode=True)
+        print("Usage:")
+        print("  python pipeline.py mcp              Run MCP server")
+        print("  python pipeline.py update           Build / refresh index")
+        print("  python pipeline.py search --query X Semantic search")

package/scaffold/cocoindex/pyproject.toml CHANGED Viewed

@@ -3,10 +3,9 @@ name = "ai-spector-cocoindex"
 version = "0.1.0"
 requires-python = ">=3.11"
 dependencies = [
-    "cocoindex>=0.3.39",
+    "cocoindex[sentence_transformers,lancedb]>=1.0.7",
     "mcp>=1.0",
-    "sentence-transformers>=3.0",
-    "lancedb>=0.8",
+    "python-dotenv>=1.0",
 ]
 [project.optional-dependencies]

package/scaffold/cocoindex/requirements.txt CHANGED Viewed

@@ -1,10 +1,9 @@
-cocoindex>=0.3.39
+cocoindex[sentence_transformers,lancedb]>=1.0.7
 mcp>=1.0
-sentence-transformers>=3.0
-lancedb>=0.8
-# Uncomment if using Postgres+pgvector (COCOINDEX_DB_URL set):
-# psycopg2-binary>=2.9
+python-dotenv>=1.0
 # Uncomment if using OpenAI embeddings (OPENAI_API_KEY set):
 # openai>=1.0
+# Uncomment if using Postgres storage (COCOINDEX_DB_URL set):
+# psycopg2-binary>=2.9

package/scaffold/cocoindex/server.py CHANGED Viewed

@@ -1,32 +1,132 @@
-"""MCP server for ai-spector CocoIndex — exposes docs_search and docs_update."""
+"""
+MCP server for ai-spector CocoIndex.
-import cocoindex
-from mcp.server.fastmcp import FastMCP
+Exposes two tools:
+  docs_search  — semantic search over indexed project docs
+  docs_update  — rebuild the index from current project docs
-from flow import search
+Embedder and LanceDB connection are kept warm for the lifetime of the server
+via FastMCP lifespan — no cold-start cost per tool call.
+"""
-mcp = FastMCP("ai-spector-cocoindex")
+from __future__ import annotations
+from contextlib import asynccontextmanager
+from dataclasses import dataclass
+from typing import AsyncIterator, TypedDict
+from mcp.server.fastmcp import Context, FastMCP
+from mcp.server.fastmcp.exceptions import ToolError
+from cocoindex.connectors import lancedb
+from cocoindex.ops.sentence_transformers import SentenceTransformerEmbedder
+from flow import EMBED_MODEL, LANCEDB_URI, TABLE_NAME, app
+# ── Lifespan state ────────────────────────────────────────────────────────────
+@dataclass
+class ServerState:
+    embedder: SentenceTransformerEmbedder
+    db: lancedb.LanceAsyncConnection
+@asynccontextmanager
+async def lifespan(server: FastMCP) -> AsyncIterator[ServerState]:
+    """Load embedder and open DB connection once; keep warm for all tool calls."""
+    embedder = SentenceTransformerEmbedder(EMBED_MODEL)
+    db = await lancedb.connect_async(LANCEDB_URI)
+    yield ServerState(embedder=embedder, db=db)
+# ── Server ────────────────────────────────────────────────────────────────────
+mcp = FastMCP("ai-spector-cocoindex", lifespan=lifespan)
+# ── Return types ──────────────────────────────────────────────────────────────
+class SearchResult(TypedDict):
+    docPath: str
+    heading: str
+    excerpt: str
+    score: float
+# ── Tools ─────────────────────────────────────────────────────────────────────
 @mcp.tool()
-def docs_search(query: str, limit: int = 5, threshold: float = 0.75) -> list[dict]:
+async def docs_search(
+    query: str,
+    ctx: Context,
+    limit: int = 5,
+    threshold: float = 0.75,
+) -> list[SearchResult]:
     """
     Semantic search over project docs by meaning, not keywords.
-    Use when the user asks about a concept, feature, or topic.
-    Returns: [{docPath, heading, excerpt, score}]
+    Use this when the user asks about a concept, feature, or topic in the project
+    docs. Prefer this over keyword search for questions like "how does X work" or
+    "what is the purpose of Y".
+    Args:
+        query: Natural-language description of the concept to search for.
+        limit: Maximum number of results to return (default 5).
+        threshold: Minimum similarity score 0–1 to include a result (default 0.75).
+    Returns:
+        List of matching doc chunks with docPath, heading, excerpt, and score.
     """
-    return search(query, limit, threshold)
+    state: ServerState = ctx.request_context.lifespan_context
+    try:
+        await ctx.info(f"Embedding query: {query!r}")
+        query_vec = await state.embedder.embed(query)
+        table = await state.db.open_table(TABLE_NAME)
+        raw = await (
+            await table.search(query_vec, vector_column_name="embedding")
+        ).limit(limit).to_list()
+    except Exception as exc:
+        raise ToolError(f"Search failed: {exc}") from exc
+    results: list[SearchResult] = [
+        SearchResult(
+            docPath=r["filename"],
+            heading=r.get("heading", ""),
+            excerpt=r["text"],
+            score=round(float(1.0 - r.get("_distance", 1.0)), 4),
+        )
+        for r in raw
+        if (1.0 - r.get("_distance", 1.0)) >= threshold
+    ]
+    await ctx.info(f"Returning {len(results)} result(s) above threshold {threshold}")
+    return results
 @mcp.tool()
-def docs_update() -> str:
+def docs_update(ctx: Context) -> str:
     """
     Rebuild the semantic index from project docs.
-    Call after adding or changing doc files before searching.
+    Run this after adding, editing, or deleting doc files so that docs_search
+    returns up-to-date results. The operation may take a minute for large doc sets.
+    Returns:
+        A message confirming the index was updated.
     """
-    cocoindex.cli.cli(["update", "--app", "flow.py"], standalone_mode=False)
-    return "Index updated."
+    try:
+        app.update_blocking(report_to_stdout=True)
+    except Exception as exc:
+        raise ToolError(f"Index update failed: {exc}") from exc
+    return "Index updated successfully."
+# ── Entry point ───────────────────────────────────────────────────────────────
 if __name__ == "__main__":
     mcp.run(transport="stdio")

package/scaffold/cursor/skills/ai-spector/SKILL.md CHANGED Viewed

@@ -12,6 +12,21 @@ description: >-
 **Workflow:** [../../WORKFLOW.md](../../WORKFLOW.md) · **Router:** [_skill-router.md](../_skill-router.md)
+## Invocation rule — MCP first, CLI fallback
+When the `ai-spector` MCP server is enabled (`.cursor/mcp.json` or `.mcp.json` lists it), **call the MCP tool** instead of shelling out to `npx ai-spector`. MCP returns structured JSON, avoids spawning a Node process, and is the preferred channel for agents.
+| Operation | MCP tool | CLI fallback |
+|-----------|----------|--------------|
+| Re-index project | `index({})` | `npx ai-spector index` |
+| Merge knowledge → graph | `graph_merge({ fromKnowledge: true })` | `npx ai-spector graph merge --from-knowledge` |
+| Validate graph | `graph_validate({})` | `npx ai-spector graph validate` |
+| Impact analysis | `graph_impact({ originId, change })` | `npx ai-spector graph impact …` |
+| Walk graph from node | `graph_query({ id, … })` | `npx ai-spector graph query <id> --json` |
+| **Analyze data-source** | *(no MCP tool — CLI only)* | `npx ai-spector analyze` |
+Use CLI **only** when: MCP server is not configured, the tool errors and MCP is unavailable, or the operation has no MCP equivalent (e.g. `analyze`).
 ## CLI and tool failure (non-negotiable)
 When `npx ai-spector` exits non-zero, required `--json` is invalid, or a required MCP/terminal step fails:
@@ -27,7 +42,7 @@ When `npx ai-spector` exits non-zero, required `--json` is invalid, or a require
 |------|------|
 | Config (languages, paths) | `.ai-spector/docflow.config.json` |
 | Graph | `.ai-spector/graph/traceability.graph.json` |
-| Query | `npx ai-spector graph query <id> --json` |
+| Query | `graph_query({ id })` MCP · fallback: `npx ai-spector graph query <id> --json` |
 | Templates | `.ai-spector/templates/` |
 | Doc output | `docs/srs/{lang.code}/` · `docs/basic-design/{lang.code}/` |

package/scaffold/cursor/skills/ai-spector-graph/SKILL.md CHANGED Viewed

@@ -36,7 +36,7 @@ Read **one** runbook under `references/` for the user’s intent, then execute i
 ```
 - [ ] Matched runbook read completely
-- [ ] CLI from project root (npx ai-spector)
+- [ ] MCP first (ai-spector server) → CLI fallback (npx ai-spector) — see ai-spector/SKILL.md#invocation-rule
 - [ ] On failure: pause; offer fix / workaround / pause per ai-spector/references/cli-failures.md
 ```

package/scaffold/cursor/skills/ai-spector-graph/references/analyze.md CHANGED Viewed

@@ -2,7 +2,7 @@
 Ingest `docs/data-source/` and commit knowledge into the traceability graph.
-The agent runs all CLI steps below — see [WORKFLOW.md](../../WORKFLOW.md).
+Step 0 (`npx ai-spector analyze`) is **CLI-only** — no MCP equivalent. Steps B (merge, validate) use **MCP when available**.
 ## Usage
@@ -48,6 +48,15 @@ Creates section/document nodes from templates. Do not ask the user to run this s
 ### B. Commit to graph
+**MCP (preferred when ai-spector server is configured):**
+```
+graph_merge({ fromKnowledge: true })
+graph_validate({})
+```
+**CLI fallback:**
 ```bash
 npx ai-spector graph merge --from-knowledge
 npx ai-spector graph validate
@@ -69,13 +78,13 @@ Update `state.json`: `analysis.lastRunAt`, `analysis.dataSource`, scope hash. Me
 - `knowledge.json` mirrors extract; graph is authoritative for `/generate-srs`.
 - Gaps recorded in `gaps.json`.
-## CLI steps — stop on first failure
+## Steps — stop on first failure
-| Step | Command |
-|------|---------|
-| 0 | `npx ai-spector analyze` |
-| B | `npx ai-spector graph merge --from-knowledge` |
-| B | `npx ai-spector graph validate` |
+| Step | MCP (preferred) | CLI fallback |
+|------|-----------------|--------------|
+| 0 | *(CLI only — no MCP tool)* | `npx ai-spector analyze` |
+| B merge | `graph_merge({ fromKnowledge: true })` | `npx ai-spector graph merge --from-knowledge` |
+| B validate | `graph_validate({})` | `npx ai-spector graph validate` |
 If any step fails, **pause** and use [cli-failures.md](../../ai-spector/references/cli-failures.md). Do not skip to generate SRS without user choice.

package/scaffold/cursor/skills/ai-spector-graph/references/impact.md CHANGED Viewed

@@ -58,15 +58,17 @@ Map regions with the same rules as below (`resolveImpactOrigins` / graph JSON).
 ### 3. Run impact per seed, unify report
-For each file/region, pick the **most specific** seed (`section` > domain > `document`). Dedupe seeds by id, then:
+For each file/region, pick the **most specific** seed (`section` > domain > `document`). Dedupe seeds by id, then run impact (MCP preferred, CLI fallback):
-```bash
-npx ai-spector graph impact <originId> --change content_change --json
 ```
-Or once for all seeds:
+graph_impact({ originId: "<id>", change: "content_change" })
+# or for all git seeds at once:
+graph_impact({ git: true, change: "content_change" })
+```
 ```bash
+# CLI fallback:
+npx ai-spector graph impact <originId> --change content_change --json
 npx ai-spector graph impact --git --change content_change --json
 ```
@@ -89,25 +91,27 @@ Gather context from the message (priority order):
 If several nodes match, pick the **most specific** seed: `section` > domain (`useCase`, `feature`, …) > `document`. If still ambiguous, ask **one** short clarifying question (never ask for raw node id format).
-## Run impact (CLI)
+## Run impact
-After resolving `originId` (one primary seed per region; run again for unrelated regions if needed):
+**Use MCP when the `ai-spector` server is configured. Fall back to CLI otherwise.**
-```bash
-npx ai-spector graph impact <originId> --change content_change --json
+### MCP (preferred)
+```
+graph_impact({ originId: "<id>", change: "content_change" })
+graph_impact({ git: true, change: "content_change" })
+graph_impact({ file: "docs/srs/3-use-cases.md", heading: "3.2 List Use Case", change: "content_change" })
 ```
-Or resolver flags (optional verification):
+### CLI fallback
 ```bash
+npx ai-spector graph impact <originId> --change content_change --json
+npx ai-spector graph impact --git --change content_change --json
 npx ai-spector graph impact --file docs/srs/3-use-cases.md --heading "3.2 List Use Case" --json
 ```
-Optional report file:
-```bash
-npx ai-spector graph impact <originId> --json -o .ai-spector/views/impact-<timestamp>.json
-```
+After resolving `originId` (one primary seed per region; run again for unrelated regions if needed):
 1. Parse JSON output:
    - `regenerate` / `review` arrays — traceability impact buckets
@@ -115,7 +119,7 @@ npx ai-spector graph impact <originId> --json -o .ai-spector/views/impact-<times
    - `truncated: true` — BFS hit the propagation cap; warn the user results may be incomplete
    - `resolvedFrom` / `gitSeeds` — which file/heading each seed came from (present with `--file` / `--heading` / `--git`)
 2. Present a table with `projectionPath` per entry.
-3. For each **regenerate** id, suggest `/generate-srs` or `/generate-basic-design` using:
+3. For each **regenerate** id, suggest `/generate-srs` or `/generate-basic-design` using MCP `graph_query({ id: "<thatId>" })` or CLI:
 ```bash
 npx ai-spector graph query <thatId> --json

package/scaffold/cursor/skills/ai-spector-graph/references/index.md CHANGED Viewed

@@ -6,8 +6,8 @@ Rebuild **graph**, re-merge **knowledge** staging, and update **document indexes
 ## Usage
-- `/index` — full CLI refresh (agent runs commands below)
-- User may run: `npx ai-spector index` with flags (see README)
+- `/index` — full refresh via MCP (preferred) or CLI fallback
+- User may run: `npx ai-spector index` with flags (see README) when MCP is unavailable
 ## When to use
@@ -19,43 +19,34 @@ Rebuild **graph**, re-merge **knowledge** staging, and update **document indexes
 **Still requires `/analyze` for:** full knowledge extraction → `knowledge.json` (NFRs, data model, rich descriptions). Index re-merges existing `knowledge.json` when present; warns if SRS changed but knowledge is stale.
-## Required Behavior (agent runs CLI)
+## Required Behavior
-```bash
-npx ai-spector index
+**Use the MCP tool when the `ai-spector` server is configured. Fall back to CLI only when MCP is unavailable.**
+### MCP (preferred)
+```
+index({})                              # full refresh
+index({ graphOnly: true })             # structure + knowledge merge only
+index({ docsOnly: true })              # doc indexes only
+index({ skipMerge: true })             # skip knowledge.json merge
+index({ skipDocSemantics: true })      # skip UC/F body parsing
 ```
-After **`/generate-srs`** (recommended):
+### CLI fallback
 ```bash
 npx ai-spector index
+npx ai-spector index --graph-only
+npx ai-spector index --docs-only
 ```
 Index steps (default): registry/bootstrap → knowledge merge → **SRS/docs body extract** → **source hub** → **provenance (`derivedFrom`)** → **business hub** → validate → doc indexes.
-**CLI alone is not full semantics:** Index builds structure + parseable meaning. For cross-hub evidence links (`relatesTo`), run **`/link-graph`** after index, then `npx ai-spector graph merge --semantic`. Check gaps with `npx ai-spector graph report --json`.
+**CLI alone is not full semantics:** Index builds structure + parseable meaning. For cross-hub evidence links (`relatesTo`), run **`/link-graph`** after index, then `graph_merge({ semantic: true })` (MCP) or `npx ai-spector graph merge --semantic`. Check gaps with `npx ai-spector graph report --json`.
 **Provenance:** UC/F/requirement/actor nodes get **`derivedFrom`** edges to `docs/data-source/**` paths (from `knowledge.json` `sourceRef` / `sourceRefs` / `derivedFrom`, SRS detail `Source:` lines, or inline `docs/data-source/…` mentions). No evidence → no edge.
-Flags:
-| Flag | Effect |
-|------|--------|
-| `--skip-doc-semantics` | Skip UC/F parsing from `docs/srs` and `docs/basic-design` |
-| `--skip-merge` | Skip `knowledge.json` merge |
-Structure + merge only:
-```bash
-npx ai-spector index --graph-only
-```
-Doc indexes only:
-```bash
-npx ai-spector index --docs-only
-```
 ## Stop on failure
 Follow [cli-failures.md](../../ai-spector/references/cli-failures.md). Do not hand-edit `traceability.graph.json` to "fix" validate errors.

package/scaffold/cursor/skills/ai-spector-graph/references/validate-graph.md CHANGED Viewed

@@ -8,12 +8,20 @@ Gate before generation. **User runs this command;** agent runs the CLI.
 ## Required Behavior
+**MCP (preferred when ai-spector server is configured):**
+```
+graph_validate({})
+```
+**CLI fallback:**
 ```bash
 npx ai-spector graph validate
 ```
-- **Exit 0** → tell the user OK; if domain nodes exist, suggest `/generate-srs`; if only section shells, explain they need `/analyze` first.
-- **Non-zero** → **stop**. Use [cli-failures.md](../../ai-spector/references/cli-failures.md): paste every `[ERROR]` line, explain each, give fix steps (usually re-run `/analyze` or fix one node then re-validate).
+- **Success / exit 0** → tell the user OK; if domain nodes exist, suggest `/generate-srs`; if only section shells, explain they need `/analyze` first.
+- **Failure / non-zero** → **stop**. Use [cli-failures.md](../../ai-spector/references/cli-failures.md): paste every `[ERROR]` line, explain each, give fix steps (usually re-run `/analyze` or fix one node then re-validate).
 **Do not:** guess validation in the agent, hand-fix the whole graph without showing the user, or proceed to `/generate-srs`.