ai-spector 0.1.7 → 0.2.0

package/README.md

@@ -4,6 +4,8 @@ Turn project notes and specs into structured documentation (SRS, basic design, d
 
 You work with **slash commands**. The AI runs the `ai-spector` CLI behind the scenes. You only use the terminal once: **`npx ai-spector init`**.
 
+Release history: [CHANGELOG.md](CHANGELOG.md).
+
 ---
 
 ## How you work (Cursor-first)
@@ -19,19 +21,19 @@ Put your source files in `docs/data-source/`, open the folder in Cursor, turn on
 
 **Graphify requires:** [uv](https://docs.astral.sh/uv/) installed; package `graphifyy` is pulled via `uv tool run` on first MCP start.
 
-### Then use slash commands
+### Slash commands
 
 | You run | What happens |
 |---------|----------------|
-| **`/analyze`** | Builds the graph skeleton, extracts knowledge (Graphify), merges use cases & features into the graph, validates |
-| **`/visualize-graph`** | Opens a browser report to inspect the graph and `knowledge.json` |
+| **`/analyze`** | Graph skeleton, Graphify extract → `knowledge.json`, merge domain nodes, validate |
 | **`/validate-graph`** | Checks the graph before generation |
-| **`/generate-srs`** | All SRS, listed files, or a short request (agent confirms scope) — graph-first, by DAG waves |
-| **`/generate-basic-design`** | All, listed files, or request (confirm) — graph + SRS context, by waves |
+| **`/generate-srs`** | SRS by DAG waves — graph-first context, `rendersTo` + `dependsOn` on output |
+| **`/generate-basic-design`** | Basic design from graph + SRS (same targeting/waves pattern) |
 | **`/generate-detail-design`** | Detail design from the graph |
-| **`/impact`** [what changed] | Shows what to regenerate after you change something (agent resolves graph seed) |
-| **`/index`** (or `ai-spector index`) | Rebuild graph structure, re-merge knowledge, Graphify storage, doc indexes after manual file edits |
-| **`/summary`** (optional) | Build `.ai-spector/index/*.md` doc summaries — not the same as full `/index` |
+| **`/index`** | Full refresh: registry/bootstrap, knowledge merge, **UC/F from markdown**, Graphify on changed paths, validate, doc indexes — run after **`/generate-srs`** |
+| **`/summary`** | Optional searchable summaries under `.ai-spector/index/` only (not a full graph refresh) |
+| **`/impact`** [what changed] | Regen scope from **your description**, git diff, selection, or path — agent resolves seeds (no node id required) |
+| **`/visualize-graph`** | Browser report: graph, knowledge, detail docs, sections, **`rendersTo`** to file paths |
 
 **Typical path:**
 
@@ -41,9 +43,10 @@ npx ai-spector init
 → /analyze
 → /validate-graph
 → /generate-srs
+→ /index
 ```
 
-Command details live in `.cursor/commands/` after `init` (start with `_workflow.md`).
+Command details live in `.cursor/commands/` after `init` — start with `_workflow.md`. Deeper guides: `index.md`, `summary.md`, `impact.md`, `analyze.md`.
 
 If a CLI step fails during a slash command, the agent should **stop**, show you the error, and help you fix it — not bypass the tool with manual edits. See `_cli-failures.md` in your project after `init`.
 
@@ -67,9 +70,12 @@ All structure and traceability live in one file:
 
 - Chapters and headings → **sections** in the graph  
 - Use cases, features, actors → **domain nodes** with links (`listedIn`, `satisfies`, …)  
-- Files under `docs/srs/` → **output** of the graph, not the source of truth  
+- Generated markdown under `docs/srs/`, `docs/basic-design/`, etc. → linked by **`rendersTo`** (target is the **repo-relative file path**, not a node id)  
+- Per-UC / per-feature **detail files** → extra `document` nodes, **section** nodes from headings, **`definedIn`** from domain nodes to those sections  
+
+**`/index`** (or `ai-spector index`) parses UC/F/actor ids from SRS and basic-design bodies and wires detail semantics without a full **`/analyze`**. **`/analyze`** is still required for rich Graphify MCP extract into `knowledge.json`.
 
-**Graphify** (optional MCP) only helps read `docs/data-source/` during **`/analyze`**. The graph remains canonical.
+**Graphify** (optional MCP) helps read `docs/data-source/` during **`/analyze`**. The graph remains canonical.
 
 ---
 
@@ -77,7 +83,7 @@ All structure and traceability live in one file:
 
 - Node.js 20+
 - [Cursor](https://cursor.com)
-- Graphify MCP for **`/analyze`**
+- Graphify MCP for **`/analyze`** (optional for **`/index`** with `--skip-graphify`)
 
 ---
 
@@ -92,7 +98,7 @@ npm install && npm run build
 npm run init:example
 ```
 
-Open **`example/`** as the Cursor workspace, add files under `example/docs/data-source/`, then run **`/analyze`** → **`/generate-srs`**.
+Open **`example/`** as the Cursor workspace, add files under `example/docs/data-source/`, then run **`/analyze`** → **`/generate-srs`** → **`/index`**.
 
 See [example/README.md](example/README.md).
 
@@ -102,19 +108,33 @@ See [example/README.md](example/README.md).
 
 ```text
 your-project/
-  .cursor/commands/          # /analyze, /generate-srs, …
+  .cursor/commands/          # /analyze, /index, /impact, …
   .cursor/skills/ai-spector/
   .ai-spector/
     graph/traceability.graph.json
     .docflow/analysis/knowledge.json
+    index/                     # optional summaries (/summary)
     views/graph-knowledge.html   # after /visualize-graph
   docs/
     data-source/                 # your inputs
-    srs/                         # generated
+    srs/                         # generated (+ per-UC/F detail files)
+    basic-design/
 ```
 
 ---
 
+## Troubleshooting
+
+| Symptom | What to try |
+|---------|-------------|
+| CLI error during a slash command | Read agent **Blocked** message; fix cause; re-run the **same** command — see `_cli-failures.md` |
+| Validate fails on `rendersTo` | Ensure each generated doc has `rendersTo` from its template `doc.*` node to the real file path; run **`/index`** after **`/generate-srs`** |
+| Stale UC/F or detail sections | **`/index`** (body extract + section `definedIn`); full knowledge refresh needs **`/analyze`** |
+| Unsure what to regenerate | **`/impact`** (empty = git diff), or describe the change in plain language |
+| Graphify unavailable | `ai-spector index --skip-graphify` |
+
+---
+
 ## For developers & contributors
 
 The CLI is the engine; Cursor commands wrap it.
@@ -123,13 +143,14 @@ The CLI is the engine; Cursor commands wrap it.
 |-----|--------|
 | [workflow-overview.md](docs/design/workflow-overview.md) | Graph-centric design |
 | [traceability-graph-redesign.md](docs/design/traceability-graph-redesign.md) | Schema and roadmap |
-| [testing.md](docs/testing.md) | Vitest layout, commands, mocking |
+| [testing.md](docs/testing.md) | Vitest, `tests/` layout, `npm test`, mocking |
 
-**Build from source:**
+**Tests:** [Vitest](https://vitest.dev/) — mirror `src/` under `tests/` (e.g. `tests/graph/InMemoryGraph.test.ts`). Do not colocate tests in `src/`.
 
 ```bash
 npm install && npm run build
-npm test
+npm test              # vitest run
+npm run test:watch    # during development
 npm run init:example
 ```
 
@@ -138,16 +159,16 @@ npm run init:example
 | Command | Purpose |
 |---------|---------|
 | `ai-spector init` | Scaffold project |
-| `ai-spector analyze` | Section tree in graph |
-| `ai-spector graphify update` | Graphify code graph → `.ai-spector/.../graphify-out/` (sets `GRAPHIFY_OUT`) |
+| `ai-spector analyze` | Section tree in graph (`--merge` if knowledge present) |
+| `ai-spector index` | Graph bootstrap, knowledge merge, doc semantics, Graphify, validate, doc indexes |
+| `ai-spector graphify update` | Graphify code graph → `.ai-spector/.../graphify-out/` |
 | `ai-spector graph merge --from-knowledge` | Domain nodes from staging |
-| `ai-spector graph validate` | Rules check |
-| `ai-spector graph visualize [--open]` | HTML report |
+| `ai-spector graph validate` | Schema + rules (`rendersTo` may target file paths) |
+| `ai-spector graph visualize [--open]` | HTML report (detail docs, sections, `rendersTo` edges) |
 | `ai-spector graph query <id> --json` | Context for generation |
-| `ai-spector graph impact <id> --json` | Regen scope (or `--file` / `--heading` / `--git` for current diff) |
-| `ai-spector index` | Refresh graph + knowledge merge + Graphify + `.ai-spector/index/` (see flags below) |
+| `ai-spector graph impact` | Regen scope — `<id>` optional with `--file`, `--heading`, or `--git` |
 
-**`ai-spector index` flags:** `--graph-only`, `--docs-only`, `--skip-graphify`, `--skip-docs`, `--skip-merge`, `--skip-validate`
+**`ai-spector index` flags:** `--graph-only`, `--docs-only`, `--skip-graphify`, `--skip-docs`, `--skip-merge`, `--skip-doc-semantics`, `--force-graphify`, `--skip-validate`
 
 Option: `-r <path>` to point at another project root.
 

package/dist/cli.js

@@ -45,6 +45,8 @@ program
     .option("--skip-graphify", "Skip Graphify update (code graph / graphify-index)")
     .option("--skip-docs", "Skip .ai-spector/index document indexes")
     .option("--skip-merge", "Skip merging knowledge.json into graph")
+    .option("--skip-doc-semantics", "Skip parsing docs/srs and docs/basic-design for UC/F/actor ids into the graph")
+    .option("--force-graphify", "Re-run Graphify update on all sources even when unchanged")
     .option("--skip-validate", "Skip graph validate after refresh")
     .action(async (opts, cmd) => {
     await runIndex({
@@ -54,6 +56,8 @@ program
         skipGraphify: opts.skipGraphify,
         skipDocs: opts.skipDocs,
         skipMerge: opts.skipMerge,
+        skipDocSemantics: opts.skipDocSemantics,
+        forceGraphify: opts.forceGraphify,
         skipValidate: opts.skipValidate,
     });
 });
@@ -71,11 +75,13 @@ graphify
     .command("update [path]")
     .description("Run graphify update on data-source with output under .ai-spector/.docflow/graph/graphify-out")
     .option("--keep-stale", "Do not delete docs/data-source/graphify-out if Graphify wrote it there by mistake")
+    .option("--force", "Re-run update on all configured sources even when content hash unchanged")
     .action(async (path, opts, cmd) => {
     await runGraphifyUpdate({
         root: projectRootOpt(cmd),
         sourcePath: path,
         removeStaleOutput: !opts.keepStale,
+        force: opts.force,
     });
 });
 const graph = program.command("graph").description("Traceability graph operations");

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package/dist/commands/graphify-update.d.ts

@@ -2,6 +2,13 @@ export interface GraphifyUpdateOptions {
     root?: string;
     sourcePath?: string;
     removeStaleOutput?: boolean;
+    /** Re-run graphify update on all configured sources even when content hash unchanged */
+    force?: boolean;
 }
-export declare function runGraphifyUpdate(opts: GraphifyUpdateOptions): Promise<void>;
+export interface GraphifyUpdateResult {
+    sourcesRun: string[];
+    sourcesSkipped: string[];
+    sourceHashes: Record<string, string>;
+}
+export declare function runGraphifyUpdate(opts?: GraphifyUpdateOptions): Promise<GraphifyUpdateResult>;
 //# sourceMappingURL=graphify-update.d.ts.map

package/dist/commands/graphify-update.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"graphify-update.d.ts","sourceRoot":"","sources":["../../src/commands/graphify-update.ts"],"names":[],"mappings":"AAeA,MAAM,WAAW,qBAAqB;IACpC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,iBAAiB,CAAC,EAAE,OAAO,CAAC;CAC7B;AAgDD,wBAAsB,iBAAiB,CAAC,IAAI,EAAE,qBAAqB,GAAG,OAAO,CAAC,IAAI,CAAC,CA6DlF"}
+{"version":3,"file":"graphify-update.d.ts","sourceRoot":"","sources":["../../src/commands/graphify-update.ts"],"names":[],"mappings":"AAmBA,MAAM,WAAW,qBAAqB;IACpC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,wFAAwF;IACxF,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACtC;AAgDD,wBAAsB,iBAAiB,CACrC,IAAI,GAAE,qBAA0B,GAC/B,OAAO,CAAC,oBAAoB,CAAC,CA2G/B"}

package/dist/commands/graphify-update.js

@@ -2,7 +2,8 @@ import { spawn } from "node:child_process";
 import { rm } from "node:fs/promises";
 import { join, resolve } from "node:path";
 import { loadDocflowConfig } from "../config/load.js";
-import { pathExists, readJson } from "../util/fs.js";
+import { filterSourcesByHashChange, resolveGraphifySources, } from "../graphify/sources.js";
+import { pathExists, readJson, writeJson } from "../util/fs.js";
 function runCommand(command, args, cwd, env) {
     return new Promise((resolvePromise, reject) => {
         const child = spawn(command, args, {
@@ -39,48 +40,85 @@ async function runGraphifyCli(args, cwd, env) {
         return { ...viaUv, command: `uv ${uvArgs.join(" ")}` };
     }
 }
-export async function runGraphifyUpdate(opts) {
+export async function runGraphifyUpdate(opts = {}) {
     const { root: projectRoot } = await loadDocflowConfig(opts.root);
     const configPath = join(projectRoot, ".ai-spector/.docflow/config/analyze.graphify.json");
     const config = await readJson(configPath);
     const g = config.graphify ?? {};
-    const sourceRel = opts.sourcePath ?? g.defaultDataSource ?? "docs/data-source";
-    const sourcePath = resolve(projectRoot, sourceRel);
     const outputPath = resolve(projectRoot, g.outputPath ?? ".ai-spector/.docflow/graph/graphify-out");
-    if (!(await pathExists(sourcePath))) {
-        throw new Error(`Data source not found: ${sourcePath}`);
+    const statePath = join(projectRoot, ".ai-spector/.docflow/state.json");
+    const state = await readJson(statePath).catch(() => ({
+        version: 1,
+        graphify: {},
+    }));
+    const graphifyState = state.graphify ?? {};
+    const storedHashes = graphifyState.sourceHashes;
+    let specs = resolveGraphifySources(g);
+    if (opts.sourcePath) {
+        specs = [{ path: opts.sourcePath, key: opts.sourcePath }];
+    }
+    const { toRun, hashes } = await filterSourcesByHashChange(projectRoot, specs, storedHashes, opts.force === true);
+    const sourcesRun = [];
+    const sourcesSkipped = specs
+        .filter((s) => !toRun.some((r) => r.key === s.key))
+        .map((s) => s.path);
+    if (toRun.length === 0) {
+        console.log("Graphify update: all sources unchanged (use --force to re-index)");
+        for (const s of specs) {
+            console.log(`  ○ ${s.path} (hash ${hashes[s.key] ?? "—"})`);
+        }
+        return { sourcesRun, sourcesSkipped, sourceHashes: hashes };
     }
     const env = {
         ...process.env,
         GRAPHIFY_OUT: outputPath,
     };
-    console.log(`Graphify update: ${sourceRel}`);
+    console.log(`Graphify update (${toRun.length} source(s), ${sourcesSkipped.length} unchanged)`);
     console.log(`  GRAPHIFY_OUT → ${g.outputPath ?? outputPath}`);
     console.log("  (do not pass --graph to graphify update — use GRAPHIFY_OUT instead)");
     console.log("");
-    const result = await runGraphifyCli(["update", sourceRel], projectRoot, env);
-    if (result.stdout.trim()) {
-        console.log(result.stdout.trimEnd());
-    }
-    if (result.stderr.trim()) {
-        console.error(result.stderr.trimEnd());
-    }
-    if (result.exitCode !== 0) {
-        console.error("");
-        console.error(`Failed: ${result.command} (exit ${result.exitCode})`);
-        throw new Error(`graphify update failed with exit code ${result.exitCode}`);
+    for (const spec of toRun) {
+        const sourcePath = resolve(projectRoot, spec.path);
+        if (!(await pathExists(sourcePath))) {
+            console.log(`  ⊘ skip ${spec.path} (not found)`);
+            continue;
+        }
+        console.log(`  ▶ ${spec.path} (hash ${hashes[spec.key] ?? "—"})`);
+        const result = await runGraphifyCli(["update", spec.path], projectRoot, env);
+        if (result.stdout.trim()) {
+            console.log(result.stdout.trimEnd());
+        }
+        if (result.stderr.trim()) {
+            console.error(result.stderr.trimEnd());
+        }
+        if (result.exitCode !== 0) {
+            console.error("");
+            console.error(`Failed: ${result.command} (exit ${result.exitCode})`);
+            throw new Error(`graphify update failed for ${spec.path} (exit ${result.exitCode})`);
+        }
+        sourcesRun.push(spec.path);
     }
     const graphJson = join(outputPath, "graph.json");
     if (!(await pathExists(graphJson))) {
         throw new Error(`Expected graph.json at ${g.graphJsonPath ?? graphJson} after update — check Graphify install (graphify or uv + graphifyy)`);
     }
-    const staleOut = join(sourcePath, "graphify-out");
+    const primaryRel = g.defaultDataSource ?? "docs/data-source";
+    const staleOut = join(resolve(projectRoot, primaryRel), "graphify-out");
     if (opts.removeStaleOutput !== false && (await pathExists(staleOut))) {
         await rm(staleOut, { recursive: true, force: true });
         console.log("");
-        console.log(`Removed stale ${sourceRel}/graphify-out/ (wrong default location)`);
+        console.log(`Removed stale ${primaryRel}/graphify-out/ (wrong default location)`);
     }
+    graphifyState.lastRunAt = new Date().toISOString();
+    graphifyState.sourceHashes = hashes;
+    graphifyState.sourcesRun = sourcesRun;
+    state.graphify = graphifyState;
+    await writeJson(statePath, state);
     console.log("");
     console.log(`OK — ${g.graphJsonPath ?? ".ai-spector/.docflow/graph/graphify-out/graph.json"}`);
+    if (sourcesSkipped.length > 0) {
+        console.log(`Skipped (unchanged): ${sourcesSkipped.join(", ")}`);
+    }
+    return { sourcesRun, sourcesSkipped, sourceHashes: hashes };
 }
 //# sourceMappingURL=graphify-update.js.map

package/dist/commands/graphify-update.js.map

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+{"version":3,"file":"graphify-update.js","sourceRoot":"","sources":["../../src/commands/graphify-update.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,oBAAoB,CAAC;AAC3C,OAAO,EAAE,EAAE,EAAE,MAAM,kBAAkB,CAAC;AACtC,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAC1C,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAC;AACtD,OAAO,EACL,yBAAyB,EACzB,sBAAsB,GAEvB,MAAM,wBAAwB,CAAC;AAChC,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAwBhE,SAAS,UAAU,CACjB,OAAe,EACf,IAAc,EACd,GAAW,EACX,GAAsB;IAEtB,OAAO,IAAI,OAAO,CAAC,CAAC,cAAc,EAAE,MAAM,EAAE,EAAE;QAC5C,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE;YACjC,GAAG;YACH,GAAG;YACH,KAAK,EAAE,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC;SAClC,CAAC,CAAC;QACH,IAAI,MAAM,GAAG,EAAE,CAAC;QAChB,IAAI,MAAM,GAAG,EAAE,CAAC;QAChB,KAAK,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,CAAC,KAAa,EAAE,EAAE;YACzC,MAAM,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;QAC7B,CAAC,CAAC,CAAC;QACH,KAAK,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,EAAE,CAAC,KAAa,EAAE,EAAE;YACzC,MAAM,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;QAC7B,CAAC,CAAC,CAAC;QACH,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC;QAC1B,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,EAAE;YACzB,cAAc,CAAC;gBACb,QAAQ,EAAE,IAAI,IAAI,CAAC;gBACnB,MAAM;gBACN,MAAM;aACP,CAAC,CAAC;QACL,CAAC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACL,CAAC;AAED,KAAK,UAAU,cAAc,CAC3B,IAAc,EACd,GAAW,EACX,GAAsB;IAEtB,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,UAAU,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;QAC5D,OAAO,EAAE,GAAG,MAAM,EAAE,OAAO,EAAE,YAAY,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;IAC9D,CAAC;IAAC,MAAM,CAAC;QACP,MAAM,MAAM,GAAG,CAAC,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,WAAW,EAAE,UAAU,EAAE,GAAG,IAAI,CAAC,CAAC;QAC3E,MAAM,KAAK,GAAG,MAAM,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;QACvD,OAAO,EAAE,GAAG,KAAK,EAAE,OAAO,EAAE,MAAM,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;IACzD,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,OAA8B,EAAE;IAEhC,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,GAAG,MAAM,iBAAiB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACjE,MAAM,UAAU,GAAG,IAAI,CAAC,WAAW,EAAE,mDAAmD,CAAC,CAAC;IAC1F,MAAM,MAAM,GAAG,MAAM,QAAQ,CAAwB,UAAU,CAAC,CAAC;IACjE,MAAM,CAAC,GAAG,MAAM,CAAC,QAAQ,IAAI,EAAE,CAAC;IAEhC,MAAM,UAAU,GAAG,OAAO,CACxB,WAAW,EACX,CAAC,CAAC,UAAU,IAAI,yCAAyC,CAC1D,CAAC;IAEF,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,iCAAiC,CAAC,CAAC;IACvE,MAAM,KAAK,GAAG,MAAM,QAAQ,CAA0B,SAAS,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC;QAC5E,OAAO,EAAE,CAAC;QACV,QAAQ,EAAE,EAAE;KACb,CAAC,CAAC,CAAC;IACJ,MAAM,aAAa,GAAI,KAAK,CAAC,QAAoC,IAAI,EAAE,CAAC;IACxE,MAAM,YAAY,GAAG,aAAa,CAAC,YAAkD,CAAC;IAEtF,IAAI,KAAK,GAAG,sBAAsB,CAAC,CAAC,CAAC,CAAC;IACtC,IAAI,IAAI,CAAC,UAAU,EAAE,CAAC;QACpB,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,UAAU,EAAE,GAAG,EAAE,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC;IAC5D,CAAC;IAED,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,MAAM,yBAAyB,CACvD,WAAW,EACX,KAAK,EACL,YAAY,EACZ,IAAI,CAAC,KAAK,KAAK,IAAI,CACpB,CAAC;IAEF,MAAM,UAAU,GAAa,EAAE,CAAC;IAChC,MAAM,cAAc,GAAG,KAAK;SACzB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;SAClD,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;IAEtB,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,CAAC,GAAG,CAAC,kEAAkE,CAAC,CAAC;QAChF,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;YACtB,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,IAAI,UAAU,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,CAAC;QAC9D,CAAC;QACD,OAAO,EAAE,UAAU,EAAE,cAAc,EAAE,YAAY,EAAE,MAAM,EAAE,CAAC;IAC9D,CAAC;IAED,MAAM,GAAG,GAAG;QACV,GAAG,OAAO,CAAC,GAAG;QACd,YAAY,EAAE,UAAU;KACzB,CAAC;IAEF,OAAO,CAAC,GAAG,CAAC,oBAAoB,KAAK,CAAC,MAAM,eAAe,cAAc,CAAC,MAAM,aAAa,CAAC,CAAC;IAC/F,OAAO,CAAC,GAAG,CAAC,oBAAoB,CAAC,CAAC,UAAU,IAAI,UAAU,EAAE,CAAC,CAAC;IAC9D,OAAO,CAAC,GAAG,CAAC,uEAAuE,CAAC,CAAC;IACrF,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;IAEhB,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,UAAU,GAAG,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC;QACnD,IAAI,CAAC,CAAC,MAAM,UAAU,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC;YACpC,OAAO,CAAC,GAAG,CAAC,YAAY,IAAI,CAAC,IAAI,cAAc,CAAC,CAAC;YACjD,SAAS;QACX,CAAC;QAED,OAAO,CAAC,GAAG,CAAC,OAAO,IAAI,CAAC,IAAI,UAAU,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,CAAC;QAClE,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,CAAC,QAAQ,EAAE,IAAI,CAAC,IAAI,CAAC,EAAE,WAAW,EAAE,GAAG,CAAC,CAAC;QAE7E,IAAI,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC;YACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,CAAC;QACvC,CAAC;QACD,IAAI,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,CAAC;YACzB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,CAAC;QACzC,CAAC;QAED,IAAI,MAAM,CAAC,QAAQ,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YAClB,OAAO,CAAC,KAAK,CAAC,WAAW,MAAM,CAAC,OAAO,UAAU,MAAM,CAAC,QAAQ,GAAG,CAAC,CAAC;YACrE,MAAM,IAAI,KAAK,CAAC,8BAA8B,IAAI,CAAC,IAAI,UAAU,MAAM,CAAC,QAAQ,GAAG,CAAC,CAAC;QACvF,CAAC;QACD,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC7B,CAAC;IAED,MAAM,SAAS,GAAG,IAAI,CAAC,UAAU,EAAE,YAAY,CAAC,CAAC;IACjD,IAAI,CAAC,CAAC,MAAM,UAAU,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC;QACnC,MAAM,IAAI,KAAK,CACb,0BAA0B,CAAC,CAAC,aAAa,IAAI,SAAS,qEAAqE,CAC5H,CAAC;IACJ,CAAC;IAED,MAAM,UAAU,GAAG,CAAC,CAAC,iBAAiB,IAAI,kBAAkB,CAAC;IAC7D,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,W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package/dist/commands/index.d.ts

@@ -12,7 +12,10 @@ export interface IndexOptions {
     skipGraphify?: boolean;
     skipDocs?: boolean;
     skipMerge?: boolean;
+    skipDocSemantics?: boolean;
     skipValidate?: boolean;
+    /** Re-run Graphify on all sources even when content hash unchanged */
+    forceGraphify?: boolean;
 }
 export interface IndexReport {
     steps: IndexStepResult[];

package/dist/commands/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/commands/index.ts"],"names":[],"mappings":"AA4BA,MAAM,MAAM,eAAe,GAAG,IAAI,GAAG,SAAS,GAAG,QAAQ,CAAC;AAE1D,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,eAAe,CAAC;IACxB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,YAAY,CAAC,EAAE,OAAO,CAAC;CACxB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,eAAe,EAAE,CAAC;IACzB,MAAM,EAAE,OAAO,CAAC;CACjB;AAED,wBAAsB,QAAQ,CAC5B,IAAI,GAAE,YAAiB,GACtB,OAAO,CAAC,WAAW,CAAC,CA+RtB"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/commands/index.ts"],"names":[],"mappings":"AAgCA,MAAM,MAAM,eAAe,GAAG,IAAI,GAAG,SAAS,GAAG,QAAQ,CAAC;AAE1D,MAAM,WAAW,eAAe;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,eAAe,CAAC;IACxB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,sEAAsE;IACtE,aAAa,CAAC,EAAE,OAAO,CAAC;CACzB;AAED,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,eAAe,EAAE,CAAC;IACzB,MAAM,EAAE,OAAO,CAAC;CACjB;AAED,wBAAsB,QAAQ,CAC5B,IAAI,GAAE,YAAiB,GACtB,OAAO,CAAC,WAAW,CAAC,CAkVtB"}

package/dist/commands/index.js

@@ -5,6 +5,7 @@ import { bootstrapFromRegistry } from "./bootstrap.js";
 import { validateGraph, formatIssues } from "./validate.js";
 import { runGraphMerge } from "./graph-merge.js";
 import { runGraphifyUpdate } from "./graphify-update.js";
+import { knowledgeStaleWarning, runDocSemanticMerge, } from "../index/doc-semantics.js";
 import { resolveProjectPaths } from "../util/paths.js";
 import { pathExists, readJson, writeJson } from "../util/fs.js";
 import { loadDocflowConfig } from "../config/load.js";
@@ -131,14 +132,65 @@ export async function runIndex(opts = {}) {
                 }
             }
         }
+        if (!opts.skipDocSemantics && !failed) {
+            try {
+                const docResult = await runDocSemanticMerge({
+                    projectRoot,
+                    graphPath: paths.graph,
+                });
+                if (docResult.merged) {
+                    graphJson = await readJson(paths.graph);
+                    const stale = await knowledgeStaleWarning(projectRoot, docResult.sourceHashes);
+                    record({
+                        id: "docs-semantic-merge",
+                        label: "SRS/docs → graph (body extract)",
+                        status: "ok",
+                        detail: stale ? `${docResult.detail}\n      ⚠ ${stale}` : docResult.detail,
+                    });
+                }
+                else {
+                    record({
+                        id: "docs-semantic-merge",
+                        label: "SRS/docs → graph (body extract)",
+                        status: "skipped",
+                        detail: docResult.detail,
+                    });
+                }
+            }
+            catch (err) {
+                record({
+                    id: "docs-semantic-merge",
+                    label: "SRS/docs → graph (body extract)",
+                    status: "failed",
+                    detail: err instanceof Error ? err.message : String(err),
+                });
+            }
+        }
+        else if (opts.skipDocSemantics) {
+            record({
+                id: "docs-semantic-merge",
+                label: "SRS/docs → graph (body extract)",
+                status: "skipped",
+                detail: "--skip-doc-semantics",
+            });
+        }
         if (runGraphify && !failed) {
             try {
-                await runGraphifyUpdate({ root: projectRoot });
+                const gf = await runGraphifyUpdate({
+                    root: projectRoot,
+                    force: opts.forceGraphify,
+                });
+                const runDetail = gf.sourcesRun.length > 0
+                    ? `updated: ${gf.sourcesRun.join(", ")}`
+                    : "no source changes";
+                const skipDetail = gf.sourcesSkipped.length > 0
+                    ? `; unchanged: ${gf.sourcesSkipped.join(", ")}`
+                    : "";
                 record({
                     id: "graphify-storage",
                     label: "Graphify index & graph.json",
                     status: "ok",
-                    detail: ".ai-spector/.docflow/graph/graphify-out/",
+                    detail: `${runDetail}${skipDetail}`,
                 });
             }
             catch (err) {
@@ -309,7 +361,8 @@ function printIndexSummary(steps, failed) {
     }
     else {
         console.log("All requested steps completed.");
-        console.log("Semantic knowledge re-extract still requires /analyze in Cursor (Graphify MCP).");
+        console.log("Full semantic re-extract (actors, NFRs, data model) still uses /analyze + Graphify MCP → knowledge.json.");
+        console.log("Index merges existing knowledge plus UC/F/actor ids parsed from docs/srs and docs/basic-design bodies.");
     }
 }
 //# sourceMappingURL=index.js.map

package/dist/commands/index.js.map

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package/dist/graph/InMemoryGraph.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"InMemoryGraph.d.ts","sourceRoot":"","sources":["../../src/graph/InMemoryGraph.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,SAAS,EAAE,iBAAiB,EAAE,eAAe,EAAE,MAAM,aAAa,CAAC;AAE5F,qBAAa,aAAa;IACxB,QAAQ,CAAC,SAAS,yBAAgC;IAClD,QAAQ,CAAC,QAAQ,2BAAkC;IACnD,QAAQ,CAAC,OAAO,2BAAkC;IAElD,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,iBAAiB,GAAG,aAAa;IAiBnD,MAAM,IAAI,iBAAiB;IAQ3B,uEAAuE;IACvE,mBAAmB,IAAI,iBAAiB;IAmBxC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAS9B,6EAA6E;IAC7E,UAAU,CAAC,IAAI,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS;IAelD,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM;IAIhC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAYjC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAU9B,eAAe,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAezC,SAAS,CACP,EAAE,EAAE,MAAM,EACV,SAAS,EAAE,KAAK,GAAG,IAAI,GAAG,MAAM,EAChC,SAAS,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACvB,KAAK,SAAI,GACR,GAAG,CAAC,MAAM,CAAC;IAsCd,iBAAiB,IAAI,eAAe,EAAE;CA+DvC"}
+{"version":3,"file":"InMemoryGraph.d.ts","sourceRoot":"","sources":["../../src/graph/InMemoryGraph.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,SAAS,EAAE,iBAAiB,EAAE,eAAe,EAAE,MAAM,aAAa,CAAC;AAE5F,qBAAa,aAAa;IACxB,QAAQ,CAAC,SAAS,yBAAgC;IAClD,QAAQ,CAAC,QAAQ,2BAAkC;IACnD,QAAQ,CAAC,OAAO,2BAAkC;IAElD,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,iBAAiB,GAAG,aAAa;IAiBnD,MAAM,IAAI,iBAAiB;IAQ3B,uEAAuE;IACvE,mBAAmB,IAAI,iBAAiB;IAmBxC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAS9B,6EAA6E;IAC7E,UAAU,CAAC,IAAI,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS;IAelD,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM;IAIhC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAYjC,OAAO,CAAC,IAAI,EAAE,SAAS,GAAG,IAAI;IAU9B,eAAe,CAAC,IAAI,EAAE,SAAS,GAAG,OAAO;IAezC,SAAS,CACP,EAAE,EAAE,MAAM,EACV,SAAS,EAAE,KAAK,GAAG,IAAI,GAAG,MAAM,EAChC,SAAS,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EACvB,KAAK,SAAI,GACR,GAAG,CAAC,MAAM,CAAC;IAsCd,iBAAiB,IAAI,eAAe,EAAE;CAsEvC"}

package/dist/graph/InMemoryGraph.js

@@ -176,6 +176,12 @@ export class InMemoryGraph {
         }
         for (const node of this.nodesById.values()) {
             if (node.type === "document") {
+                const isPerDomainInstance = typeof node.output === "string" &&
+                    !node.outputPattern &&
+                    (node.perDomain === "useCase" || node.perDomain === "feature");
+                if (isPerDomainInstance) {
+                    continue;
+                }
                 const hasSection = [...this.outEdges.get(node.id) ?? []].some((e) => e.type === "contains" &&
                     this.nodesById.get(e.to)?.type === "section");
                 if (!hasSection) {

package/dist/graph/InMemoryGraph.js.map

@@ -1 +1 @@
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