ai-spector 0.1.7 → 0.1.8

package/README.md

@@ -30,7 +30,7 @@ Put your source files in `docs/data-source/`, open the folder in Cursor, turn on
 | **`/generate-basic-design`** | All, listed files, or request (confirm) — graph + SRS context, by waves |
 | **`/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 |
+| **`/index`** (or `ai-spector index`) | Rebuild graph, merge knowledge, parse UC/F from SRS bodies, Graphify on changed paths, doc indexes — run after `/generate-srs` |
 | **`/summary`** (optional) | Build `.ai-spector/index/*.md` doc summaries — not the same as full `/index` |
 
 **Typical path:**
@@ -145,9 +145,9 @@ npm run init:example
 | `ai-spector graph visualize [--open]` | HTML report |
 | `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 index` | Refresh graph + knowledge merge + SRS body extract + Graphify + `.ai-spector/index/` (see flags below) |
 
-**`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");

package/dist/cli.js.map

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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/doc-extract.d.ts

@@ -0,0 +1,37 @@
+import type { ExtractPatch } from "./knowledge.js";
+export interface DocExtractEntry {
+    relativePath: string;
+    content: string;
+}
+export interface DocExtractResult {
+    useCases: number;
+    features: number;
+    actors: number;
+    filesScanned: number;
+}
+/** Normalize UC-1 → UC-01, F-2 → F-02; leaves placeholders (UC-XX) unchanged */
+export declare function normalizeDomainId(raw: string): string;
+interface ParsedDomain {
+    useCases: Map<string, {
+        title?: string;
+    }>;
+    features: Map<string, {
+        title?: string;
+    }>;
+    actors: Map<string, {
+        title?: string;
+    }>;
+    satisfies: Array<{
+        from: string;
+        to: string;
+    }>;
+}
+export declare function extractDomainFromMarkdown(content: string, relativePath: string): ParsedDomain;
+export declare function parsedDomainToPatch(parsed: ParsedDomain, relativePath: string): ExtractPatch;
+export declare function mergeParsedDomains(domains: ParsedDomain[]): ParsedDomain;
+export declare function buildDocExtractPatch(entries: DocExtractEntry[]): {
+    patch: ExtractPatch;
+    stats: DocExtractResult;
+};
+export {};
+//# sourceMappingURL=doc-extract.d.ts.map

package/dist/graph/doc-extract.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"doc-extract.d.ts","sourceRoot":"","sources":["../../src/graph/doc-extract.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAEnD,MAAM,WAAW,eAAe;IAC9B,YAAY,EAAE,MAAM,CAAC;IACrB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,gBAAgB;IAC/B,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;CACtB;AAWD,gFAAgF;AAChF,wBAAgB,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAcrD;AA0BD,UAAU,YAAY;IACpB,QAAQ,EAAE,GAAG,CAAC,MAAM,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC1C,QAAQ,EAAE,GAAG,CAAC,MAAM,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC1C,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACxC,SAAS,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,EAAE,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CAChD;AAmDD,wBAAgB,yBAAyB,CACvC,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,GACnB,YAAY,CA2Ed;AAUD,wBAAgB,mBAAmB,CACjC,MAAM,EAAE,YAAY,EACpB,YAAY,EAAE,MAAM,GACnB,YAAY,CAsDd;AAED,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,YAAY,EAAE,GAAG,YAAY,CAexE;AAED,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,eAAe,EAAE,GAAG;IAChE,KAAK,EAAE,YAAY,CAAC;IACpB,KAAK,EAAE,gBAAgB,CAAC;CACzB,CA2CA"}

package/dist/graph/doc-extract.js

@@ -0,0 +1,278 @@
+import { DEFAULT_LISTED_IN } from "./defaults.js";
+const UC_ID_RE = /\b(UC-\d+)\b/gi;
+const F_ID_RE = /\b(F-\d+)\b/gi;
+const USE_CASE_ID_LINE = /\*\*Use Case ID:\*\*\s*(UC-\d+)/i;
+const USE_CASE_NAME_LINE = /\*\*Use Case Name:\*\*\s*(.+)/i;
+const FEATURE_NAME_HEADING = /^#{1,3}\s+(F-\d+)\s*[:\-–—]\s*(.+)$/im;
+const UC_HEADING = /^#{1,3}\s+(UC-\d+)\s*[:\-–—]\s*(.+)$/im;
+const TABLE_ROW_UC = /^\|\s*(UC-\d+)\s*\|/im;
+const TABLE_ROW_F = /^\|\s*(F-\d+)\s*\|/im;
+/** Normalize UC-1 → UC-01, F-2 → F-02; leaves placeholders (UC-XX) unchanged */
+export function normalizeDomainId(raw) {
+    const t = raw.trim();
+    if (/XX$/i.test(t)) {
+        return t;
+    }
+    const uc = t.match(/^UC-(\d+)$/i);
+    if (uc) {
+        return `UC-${uc[1].padStart(2, "0")}`;
+    }
+    const f = t.match(/^F-(\d+)$/i);
+    if (f) {
+        return `F-${f[1].padStart(2, "0")}`;
+    }
+    return t;
+}
+function isRealDomainId(id) {
+    return /^(UC|F)-\d+$/i.test(id) && !/XX$/i.test(id);
+}
+function listedInForPath(relativePath, kind) {
+    const p = relativePath.replace(/\\/g, "/").toLowerCase();
+    if (kind === "useCase") {
+        if (p.includes("use-case") || p.includes("use-cases") || /\/3-/.test(p)) {
+            return DEFAULT_LISTED_IN.useCase;
+        }
+    }
+    if (kind === "feature") {
+        if (p.includes("system-features") || p.includes("04-system-features") || /\/4-/.test(p)) {
+            return DEFAULT_LISTED_IN.feature;
+        }
+    }
+    if (kind === "actor") {
+        if (p.includes("overall-description") || /\/2-/.test(p)) {
+            return DEFAULT_LISTED_IN.actor;
+        }
+    }
+    return DEFAULT_LISTED_IN[kind];
+}
+function emptyParsed() {
+    return {
+        useCases: new Map(),
+        features: new Map(),
+        actors: new Map(),
+        satisfies: [],
+    };
+}
+function addUseCase(parsed, id, title) {
+    const norm = normalizeDomainId(id);
+    const prev = parsed.useCases.get(norm);
+    if (!prev?.title && title?.trim()) {
+        parsed.useCases.set(norm, { title: title.trim() });
+    }
+    else if (!prev) {
+        parsed.useCases.set(norm, { title: title?.trim() });
+    }
+}
+function addFeature(parsed, id, title) {
+    const norm = normalizeDomainId(id);
+    const prev = parsed.features.get(norm);
+    if (!prev?.title && title?.trim()) {
+        parsed.features.set(norm, { title: title.trim() });
+    }
+    else if (!prev) {
+        parsed.features.set(norm, { title: title?.trim() });
+    }
+}
+function parseTableSatisfies(line, parsed) {
+    const cells = line
+        .split("|")
+        .map((c) => c.trim())
+        .filter(Boolean);
+    if (cells.length < 2) {
+        return;
+    }
+    const fMatch = cells[0]?.match(/^F-(\d+)$/i);
+    if (!fMatch) {
+        return;
+    }
+    const from = normalizeDomainId(cells[0]);
+    for (const cell of cells.slice(1)) {
+        for (const m of cell.matchAll(UC_ID_RE)) {
+            parsed.satisfies.push({ from, to: normalizeDomainId(m[1]) });
+        }
+    }
+}
+export function extractDomainFromMarkdown(content, relativePath) {
+    const parsed = emptyParsed();
+    const lines = content.split(/\r?\n/);
+    let pendingUcId;
+    for (let i = 0; i < lines.length; i++) {
+        const line = lines[i];
+        const ucIdLine = line.match(USE_CASE_ID_LINE);
+        if (ucIdLine) {
+            pendingUcId = normalizeDomainId(ucIdLine[1]);
+            addUseCase(parsed, pendingUcId);
+            continue;
+        }
+        if (pendingUcId) {
+            const nameLine = line.match(USE_CASE_NAME_LINE);
+            if (nameLine) {
+                addUseCase(parsed, pendingUcId, nameLine[1]);
+                pendingUcId = undefined;
+                continue;
+            }
+            if (line.startsWith("### ") || line.startsWith("## ")) {
+                pendingUcId = undefined;
+            }
+        }
+        const ucHeading = line.match(UC_HEADING);
+        if (ucHeading) {
+            addUseCase(parsed, ucHeading[1], ucHeading[2]);
+        }
+        const fHeading = line.match(FEATURE_NAME_HEADING);
+        if (fHeading) {
+            addFeature(parsed, fHeading[1], fHeading[2]);
+        }
+        const ucRow = line.match(TABLE_ROW_UC);
+        if (ucRow) {
+            const cells = line.split("|").map((c) => c.trim());
+            const title = cells[2] || cells[1];
+            addUseCase(parsed, ucRow[1], title && !/^UC-/i.test(title) ? title : undefined);
+        }
+        const fRow = line.match(TABLE_ROW_F);
+        if (fRow) {
+            const cells = line.split("|").map((c) => c.trim());
+            const title = cells[2] || cells[1];
+            addFeature(parsed, fRow[1], title && !/^F-/i.test(title) ? title : undefined);
+            parseTableSatisfies(line, parsed);
+        }
+        else if (/^\|.*F-\d+/i.test(line) && /UC-/i.test(line)) {
+            parseTableSatisfies(line, parsed);
+        }
+    }
+    for (const m of content.matchAll(UC_ID_RE)) {
+        if (m[1] && isRealDomainId(m[1])) {
+            addUseCase(parsed, m[1]);
+        }
+    }
+    for (const m of content.matchAll(F_ID_RE)) {
+        if (m[1] && isRealDomainId(m[1])) {
+            addFeature(parsed, m[1]);
+        }
+    }
+    const actorSection = /(?:\*\*Primary Actor:\*\*|Primary Actor:)\s*\*?\*?\s*([^\n*]+)/gi;
+    for (const m of content.matchAll(actorSection)) {
+        const name = m[1]?.trim();
+        if (name && !/^tbd$/i.test(name) && name.length > 1) {
+            const id = `actor.${slugActorId(name)}`;
+            parsed.actors.set(id, { title: name });
+        }
+    }
+    return parsed;
+}
+function slugActorId(name) {
+    return name
+        .toLowerCase()
+        .replace(/[^a-z0-9]+/g, "-")
+        .replace(/^-|-$/g, "")
+        .slice(0, 48) || "unknown";
+}
+export function parsedDomainToPatch(parsed, relativePath) {
+    const nodes = [];
+    const edges = [];
+    for (const [id, meta] of parsed.useCases) {
+        const node = { id, type: "useCase", title: meta.title ?? id };
+        if (meta.title) {
+            node.description = meta.title;
+        }
+        nodes.push(node);
+        edges.push({
+            type: "listedIn",
+            from: id,
+            to: listedInForPath(relativePath, "useCase"),
+        });
+    }
+    for (const [id, meta] of parsed.features) {
+        const node = { id, type: "feature", title: meta.title ?? id };
+        nodes.push(node);
+        edges.push({
+            type: "listedIn",
+            from: id,
+            to: listedInForPath(relativePath, "feature"),
+        });
+    }
+    for (const [id, meta] of parsed.actors) {
+        nodes.push({
+            id,
+            type: "actor",
+            title: meta.title ?? id,
+            name: meta.title,
+        });
+        edges.push({
+            type: "describedIn",
+            from: id,
+            to: listedInForPath(relativePath, "actor"),
+        });
+    }
+    const seenSatisfies = new Set();
+    for (const { from, to } of parsed.satisfies) {
+        const key = `${from}->${to}`;
+        if (seenSatisfies.has(key)) {
+            continue;
+        }
+        seenSatisfies.add(key);
+        if (parsed.features.has(from) && parsed.useCases.has(to)) {
+            edges.push({ type: "satisfies", from, to });
+        }
+    }
+    return { version: 1, nodes, edges };
+}
+export function mergeParsedDomains(domains) {
+    const out = emptyParsed();
+    for (const d of domains) {
+        for (const [id, meta] of d.useCases) {
+            addUseCase(out, id, meta.title);
+        }
+        for (const [id, meta] of d.features) {
+            addFeature(out, id, meta.title);
+        }
+        for (const [id, meta] of d.actors) {
+            out.actors.set(id, meta);
+        }
+        out.satisfies.push(...d.satisfies);
+    }
+    return out;
+}
+export function buildDocExtractPatch(entries) {
+    const perFile = [];
+    for (const e of entries) {
+        perFile.push(extractDomainFromMarkdown(e.content, e.relativePath));
+    }
+    const merged = mergeParsedDomains(perFile);
+    const allNodes = [];
+    const allEdges = [];
+    const edgeKeys = new Set();
+    for (const e of entries) {
+        const single = extractDomainFromMarkdown(e.content, e.relativePath);
+        const patch = parsedDomainToPatch(single, e.relativePath);
+        for (const n of patch.nodes) {
+            if (!allNodes.some((x) => x.id === n.id && x.type === n.type)) {
+                allNodes.push(n);
+            }
+            else {
+                const idx = allNodes.findIndex((x) => x.id === n.id);
+                const existing = allNodes[idx];
+                if (!existing.title && n.title) {
+                    allNodes[idx] = { ...existing, ...n };
+                }
+            }
+        }
+        for (const edge of patch.edges) {
+            const key = `${edge.type}:${edge.from}:${edge.to}`;
+            if (!edgeKeys.has(key)) {
+                edgeKeys.add(key);
+                allEdges.push(edge);
+            }
+        }
+    }
+    return {
+        patch: { version: 1, nodes: allNodes, edges: allEdges },
+        stats: {
+            useCases: merged.useCases.size,
+            features: merged.features.size,
+            actors: merged.actors.size,
+            filesScanned: entries.length,
+        },
+    };
+}
+//# sourceMappingURL=doc-extract.js.map

package/dist/graph/doc-extract.js.map

@@ -0,0 +1 @@
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package/dist/graphify/sources.d.ts

@@ -0,0 +1,23 @@
+export interface SourceFileFingerprint {
+    relativePath: string;
+    contentHash: string;
+}
+export declare function discoverSourceFingerprints(projectRoot: string, sourceRoot: string): Promise<SourceFileFingerprint[]>;
+export interface GraphifySourceSpec {
+    /** CLI path relative to project root */
+    path: string;
+    /** Key for state.graphify.sourceHashes */
+    key: string;
+}
+export interface GraphifySourcesConfig {
+    defaultDataSource?: string;
+    include?: string[];
+    docSources?: string[];
+}
+export declare function resolveGraphifySources(config: GraphifySourcesConfig): GraphifySourceSpec[];
+export declare function computeSourceContentHash(projectRoot: string, sourceRel: string): Promise<string | undefined>;
+export declare function filterSourcesByHashChange(projectRoot: string, specs: GraphifySourceSpec[], storedHashes: Record<string, string> | undefined, force: boolean): Promise<{
+    toRun: GraphifySourceSpec[];
+    hashes: Record<string, string>;
+}>;
+//# sourceMappingURL=sources.d.ts.map

package/dist/graphify/sources.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"sources.d.ts","sourceRoot":"","sources":["../../src/graphify/sources.ts"],"names":[],"mappings":"AAOA,MAAM,WAAW,qBAAqB;IACpC,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,wBAAsB,0BAA0B,CAC9C,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,qBAAqB,EAAE,CAAC,CAiClC;AAED,MAAM,WAAW,kBAAkB;IACjC,wCAAwC;IACxC,IAAI,EAAE,MAAM,CAAC;IACb,0CAA0C;IAC1C,GAAG,EAAE,MAAM,CAAC;CACb;AAED,MAAM,WAAW,qBAAqB;IACpC,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;CACvB;AAED,wBAAgB,sBAAsB,CACpC,MAAM,EAAE,qBAAqB,GAC5B,kBAAkB,EAAE,CAwBtB;AAED,wBAAsB,wBAAwB,CAC5C,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAW7B;AAED,wBAAsB,yBAAyB,CAC7C,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,kBAAkB,EAAE,EAC3B,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,EAChD,KAAK,EAAE,OAAO,GACb,OAAO,CAAC;IAAE,KAAK,EAAE,kBAAkB,EAAE,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;CAAE,CAAC,CAgB1E"}

package/dist/graphify/sources.js

@@ -0,0 +1,87 @@
+import { createHash } from "node:crypto";
+import { readdir, readFile } from "node:fs/promises";
+import { join, relative, resolve } from "node:path";
+import { pathExists } from "../util/fs.js";
+const SKIP_DIRS = new Set(["node_modules", ".git", "graphify-out", ".ai-spector"]);
+export async function discoverSourceFingerprints(projectRoot, sourceRoot) {
+    const rootAbs = resolve(projectRoot, sourceRoot);
+    const files = [];
+    async function walk(dir) {
+        let entries;
+        try {
+            entries = await readdir(dir, { withFileTypes: true });
+        }
+        catch {
+            return;
+        }
+        for (const ent of entries) {
+            const abs = join(dir, ent.name);
+            if (ent.isDirectory()) {
+                if (ent.name.startsWith(".") || SKIP_DIRS.has(ent.name)) {
+                    continue;
+                }
+                await walk(abs);
+                continue;
+            }
+            if (!ent.isFile()) {
+                continue;
+            }
+            const rel = relative(projectRoot, abs).replace(/\\/g, "/");
+            const raw = await readFile(abs);
+            const contentHash = createHash("sha256").update(raw).digest("hex").slice(0, 16);
+            files.push({ relativePath: rel, contentHash });
+        }
+    }
+    await walk(rootAbs);
+    files.sort((a, b) => a.relativePath.localeCompare(b.relativePath));
+    return files;
+}
+export function resolveGraphifySources(config) {
+    const seen = new Set();
+    const out = [];
+    const add = (path) => {
+        const norm = path.replace(/\\/g, "/").replace(/\/$/, "");
+        if (seen.has(norm)) {
+            return;
+        }
+        seen.add(norm);
+        out.push({ path: norm, key: norm });
+    };
+    const primary = config.defaultDataSource ?? "docs/data-source";
+    add(primary);
+    for (const p of config.include ?? []) {
+        add(p);
+    }
+    for (const p of config.docSources ?? []) {
+        add(p);
+    }
+    return out;
+}
+export async function computeSourceContentHash(projectRoot, sourceRel) {
+    const abs = resolve(projectRoot, sourceRel);
+    if (!(await pathExists(abs))) {
+        return undefined;
+    }
+    const files = await discoverSourceFingerprints(projectRoot, sourceRel);
+    if (files.length === 0) {
+        return createHash("sha256").update(`empty:${sourceRel}`).digest("hex").slice(0, 16);
+    }
+    const payload = files.map((f) => `${f.relativePath}:${f.contentHash}`).join("\n");
+    return createHash("sha256").update(payload).digest("hex").slice(0, 16);
+}
+export async function filterSourcesByHashChange(projectRoot, specs, storedHashes, force) {
+    const hashes = { ...storedHashes };
+    const toRun = [];
+    for (const spec of specs) {
+        const hash = await computeSourceContentHash(projectRoot, spec.path);
+        if (hash === undefined) {
+            continue;
+        }
+        hashes[spec.key] = hash;
+        if (force || storedHashes?.[spec.key] !== hash) {
+            toRun.push(spec);
+        }
+    }
+    return { toRun, hashes };
+}
+//# sourceMappingURL=sources.js.map

package/dist/graphify/sources.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sources.js","sourceRoot":"","sources":["../../src/graphify/sources.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AACzC,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAQ,MAAM,kBAAkB,CAAC;AAC3D,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAE3C,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,CAAC,cAAc,EAAE,MAAM,EAAE,cAAc,EAAE,aAAa,CAAC,CAAC,CAAC;AAOnF,MAAM,CAAC,KAAK,UAAU,0BAA0B,CAC9C,WAAmB,EACnB,UAAkB;IAElB,MAAM,OAAO,GAAG,OAAO,CAAC,WAAW,EAAE,UAAU,CAAC,CAAC;IACjD,MAAM,KAAK,GAA4B,EAAE,CAAC;IAE1C,KAAK,UAAU,IAAI,CAAC,GAAW;QAC7B,IAAI,OAAO,CAAC;QACZ,IAAI,CAAC;YACH,OAAO,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;QACxD,CAAC;QAAC,MAAM,CAAC;YACP,OAAO;QACT,CAAC;QACD,KAAK,MAAM,GAAG,IAAI,OAAO,EAAE,CAAC;YAC1B,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC;YAChC,IAAI,GAAG,CAAC,WAAW,EAAE,EAAE,CAAC;gBACtB,IAAI,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;oBACxD,SAAS;gBACX,CAAC;gBACD,MAAM,IAAI,CAAC,GAAG,CAAC,CAAC;gBAChB,SAAS;YACX,CAAC;YACD,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,EAAE,CAAC;gBAClB,SAAS;YACX,CAAC;YACD,MAAM,GAAG,GAAG,QAAQ,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;YAC3D,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,GAAG,CAAC,CAAC;YAChC,MAAM,WAAW,GAAG,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAChF,KAAK,CAAC,IAAI,CAAC,EAAE,YAAY,EAAE,GAAG,EAAE,WAAW,EAAE,CAAC,CAAC;QACjD,CAAC;IACH,CAAC;IAED,MAAM,IAAI,CAAC,OAAO,CAAC,CAAC;IACpB,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC;IACnE,OAAO,KAAK,CAAC;AACf,CAAC;AAeD,MAAM,UAAU,sBAAsB,CACpC,MAA6B;IAE7B,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;IAC/B,MAAM,GAAG,GAAyB,EAAE,CAAC;IAErC,MAAM,GAAG,GAAG,CAAC,IAAY,EAAE,EAAE;QAC3B,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;QACzD,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;YACnB,OAAO;QACT,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACf,GAAG,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC;IACtC,CAAC,CAAC;IAEF,MAAM,OAAO,GAAG,MAAM,CAAC,iBAAiB,IAAI,kBAAkB,CAAC;IAC/D,GAAG,CAAC,OAAO,CAAC,CAAC;IAEb,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,IAAI,EAAE,EAAE,CAAC;QACrC,GAAG,CAAC,CAAC,CAAC,CAAC;IACT,CAAC;IACD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,UAAU,IAAI,EAAE,EAAE,CAAC;QACxC,GAAG,CAAC,CAAC,CAAC,CAAC;IACT,CAAC;IAED,OAAO,GAAG,CAAC;AACb,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAC5C,WAAmB,EACnB,SAAiB;IAEjB,MAAM,GAAG,GAAG,OAAO,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;IAC5C,IAAI,CAAC,CAAC,MAAM,UAAU,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;QAC7B,OAAO,SAAS,CAAC;IACnB,CAAC;IACD,MAAM,KAAK,GAAG,MAAM,0BAA0B,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;IACvE,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvB,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,SAAS,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;IACtF,CAAC;IACD,MAAM,OAAO,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,YAAY,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAClF,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;AACzE,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,yBAAyB,CAC7C,WAAmB,EACnB,KAA2B,EAC3B,YAAgD,EAChD,KAAc;IAEd,MAAM,MAAM,GAA2B,EAAE,GAAG,YAAY,EAAE,CAAC;IAC3D,MAAM,KAAK,GAAyB,EAAE,CAAC;IAEvC,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,IAAI,GAAG,MAAM,wBAAwB,CAAC,WAAW,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC;QACpE,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,SAAS;QACX,CAAC;QACD,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC;QACxB,IAAI,KAAK,IAAI,YAAY,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC;YAC/C,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACnB,CAAC;IACH,CAAC;IAED,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;AAC3B,CAAC"}

package/dist/index/doc-semantics.d.ts

@@ -0,0 +1,14 @@
+import { type IndexDocsConfig } from "./docs-config.js";
+export interface DocSemanticMergeOptions {
+    projectRoot: string;
+    graphPath: string;
+    config?: IndexDocsConfig;
+}
+export interface DocSemanticMergeResult {
+    merged: boolean;
+    detail: string;
+    sourceHashes: Record<string, string>;
+}
+export declare function runDocSemanticMerge(opts: DocSemanticMergeOptions): Promise<DocSemanticMergeResult>;
+export declare function knowledgeStaleWarning(projectRoot: string, docHashes: Record<string, string>): Promise<string | undefined>;
+//# sourceMappingURL=doc-semantics.d.ts.map

package/dist/index/doc-semantics.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"doc-semantics.d.ts","sourceRoot":"","sources":["../../src/index/doc-semantics.ts"],"names":[],"mappings":"AASA,OAAO,EAAuB,KAAK,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAG7E,MAAM,WAAW,uBAAuB;IACtC,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,eAAe,CAAC;CAC1B;AAED,MAAM,WAAW,sBAAsB;IACrC,MAAM,EAAE,OAAO,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACtC;AAED,wBAAsB,mBAAmB,CACvC,IAAI,EAAE,uBAAuB,GAC5B,OAAO,CAAC,sBAAsB,CAAC,CA2EjC;AAED,wBAAsB,qBAAqB,CACzC,WAAW,EAAE,MAAM,EACnB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAChC,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAwB7B"}

package/dist/index/doc-semantics.js

@@ -0,0 +1,86 @@
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
+import { mergePatch } from "../graph/merge.js";
+import { loadInMemoryGraph } from "../graph/loadGraph.js";
+import { buildDocExtractPatch } from "../graph/doc-extract.js";
+import { computeIndexSourceHash, discoverMarkdownFiles, } from "./docs-build.js";
+import { indexDocsConfigPath } from "./docs-config.js";
+import { pathExists, readJson, writeJson } from "../util/fs.js";
+export async function runDocSemanticMerge(opts) {
+    const configPath = indexDocsConfigPath(opts.projectRoot);
+    if (!(await pathExists(configPath))) {
+        return {
+            merged: false,
+            detail: `Missing ${configPath}`,
+            sourceHashes: {},
+        };
+    }
+    const config = opts.config ?? (await readJson(configPath));
+    const entries = [];
+    const sourceHashes = {};
+    for (const key of ["srs", "basicDesign"]) {
+        const source = config.sources[key];
+        if (!source?.root) {
+            continue;
+        }
+        const files = await discoverMarkdownFiles(opts.projectRoot, source.root, source.glob ?? "**/*.md");
+        sourceHashes[key] = computeIndexSourceHash(files);
+        for (const f of files) {
+            const content = await readFile(join(opts.projectRoot, f.relativePath), "utf8");
+            entries.push({ relativePath: f.relativePath, content });
+        }
+    }
+    if (entries.length === 0) {
+        return {
+            merged: false,
+            detail: "No markdown under docs/srs or docs/basic-design",
+            sourceHashes,
+        };
+    }
+    const { patch, stats } = buildDocExtractPatch(entries);
+    if (patch.nodes.length === 0 && patch.edges.length === 0) {
+        return {
+            merged: false,
+            detail: `Scanned ${stats.filesScanned} files — no UC/F/actor ids found in body text`,
+            sourceHashes,
+        };
+    }
+    const graph = await loadInMemoryGraph(opts.graphPath);
+    const { stats: mergeStats } = mergePatch(graph, patch);
+    await writeJson(opts.graphPath, graph.toTraceabilityGraph());
+    const statePath = join(opts.projectRoot, ".ai-spector/.docflow/state.json");
+    const state = await readJson(statePath).catch(() => ({
+        version: 1,
+        docsSemantic: {},
+    }));
+    const docsSemantic = state.docsSemantic ?? {};
+    docsSemantic.lastRunAt = new Date().toISOString();
+    docsSemantic.sourceHashes = sourceHashes;
+    docsSemantic.lastStats = stats;
+    state.docsSemantic = docsSemantic;
+    await writeJson(statePath, state);
+    return {
+        merged: true,
+        detail: `${stats.filesScanned} files → ${stats.useCases} use cases, ${stats.features} features, ${stats.actors} actors` +
+            ` (+${mergeStats.nodesCreated} nodes, ~${mergeStats.nodesUpdated} updated, +${mergeStats.edgesAdded} edges)`,
+        sourceHashes,
+    };
+}
+export async function knowledgeStaleWarning(projectRoot, docHashes) {
+    const knowledgePath = join(projectRoot, ".ai-spector/.docflow/analysis/knowledge.json");
+    if (!(await pathExists(knowledgePath))) {
+        return undefined;
+    }
+    const statePath = join(projectRoot, ".ai-spector/.docflow/state.json");
+    const state = await readJson(statePath).catch(() => null);
+    const indexHashes = state?.index
+        ?.sourceHashes;
+    if (!indexHashes?.srs || !docHashes.srs) {
+        return undefined;
+    }
+    if (indexHashes.srs === docHashes.srs) {
+        return undefined;
+    }
+    return ("docs/srs changed since last index — knowledge.json may be stale; run /analyze for full Graphify MCP re-extract, or rely on doc semantic merge from file bodies");
+}
+//# sourceMappingURL=doc-semantics.js.map

package/dist/index/doc-semantics.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ai-spector",
-  "version": "0.1.7",
+  "version": "0.1.8",
   "description": "Cursor-first documentation workflow: traceability graph, SRS/basic/detail design templates, and ai-spector CLI",
   "type": "module",
   "license": "MIT",

package/scaffold/.ai-spector/.docflow/config/analyze.graphify.json

@@ -15,6 +15,10 @@
     "include": [
       "docs/data-source"
     ],
+    "docSources": [
+      "docs/srs",
+      "docs/basic-design"
+    ],
     "exclude": [
       ".git/**",
       "node_modules/**",
@@ -22,8 +26,6 @@
       "build/**",
       ".next/**",
       "coverage/**",
-      "docs/srs/**",
-      "docs/basic-design/**",
       "docs/detail-design/**",
       "docs/data-source/graphify-out/**",
       "**/graphify-out/**",

package/scaffold/.cursor/commands/_cli-failures.md

@@ -112,10 +112,11 @@ When any `ai-spector` command **fails** (non-zero exit, throws, or empty/invalid
 - **Means:** Changed paths are not linked to `document` / `section` nodes (e.g. only `README.md` or `src/`).
 - **Fix:** Run impact on doc paths under `docs/` or `.ai-spector/`; or **`/impact`** with a short description of the traceability change.
 
-### Stale graph or indexes after manual edits
+### Stale graph or indexes after manual edits or `/generate-srs`
 
-- **Means:** User changed `docs/data-source/`, SRS outputs, or templates without re-running ingest.
-- **Fix:** Run **`ai-spector index`** (or **`/index`** in Cursor). For semantic re-extract of actors/use cases, still run **`/analyze`** after index fixes structure.
+- **Means:** User changed `docs/data-source/`, SRS outputs, or templates without re-running ingest; graph still shows template-only domain nodes.
+- **Fix:** Run **`ai-spector index`** (or **`/index`**). Index merges `knowledge.json`, parses UC/F/actor ids from `docs/srs/` bodies, and runs Graphify on **changed** paths (`docs/data-source`, `docs/srs`, `docs/basic-design`). Use **`--force-graphify`** if Graphify output must rebuild entirely.
+- **Still stale domain detail?** Re-run **`/analyze`** for Graphify MCP → fresh `knowledge.json`.
 
 ### Graphify wrote `docs/data-source/graphify-out/`
 

package/scaffold/.cursor/commands/_workflow.md

@@ -21,7 +21,7 @@ Add source material under `docs/data-source/`, open the project in Cursor, **rel
 | 2 | **`/validate-graph`** | `ai-spector graph validate` |
 | 3 | **`/generate-srs`** [paths or request] — all, listed files, or described scope (**confirm** if described) → waves → merge (see `generate-srs.md`) |
 | 4 | **`/summary srs`** (optional) | Doc summaries under `.ai-spector/index/` (fallback browse; graph is primary) |
-| — | **`/index`** | After manual edits: `ai-spector index` (graph + knowledge merge + Graphify + doc indexes) |
+| — | **`/index`** | After manual edits or **`/generate-srs`**: `ai-spector index` (structure + knowledge merge + **SRS body extract** + Graphify on changed paths + doc indexes) |
 | 5 | **`/generate-basic-design`** [paths or request] — same targeting + waves as SRS (`generate-basic-design.md`) |
 | 6 | **`/generate-detail-design`** | same `graph query` pattern |
 | After edits | **`/impact`** [what changed] | Empty args → `git diff` + resolve seeds; else describe change → `graph impact <id> --json` (or `--git` / `--file`) |
@@ -37,6 +37,7 @@ docs/data-source/            ← add files
 /analyze
 /validate-graph
 /generate-srs
+/index
 ```
 
 ## If something fails

package/scaffold/.cursor/commands/generate-srs.md

@@ -146,6 +146,13 @@ Append to `.ai-spector/.docflow/logs/generate-srs.log` (create if needed): times
 ### 4. Finish
 
 - Final `ai-spector graph validate`.
+- **Refresh indexes and semantic graph** (parses UC/F/actor ids from generated markdown + updates Graphify on changed paths):
+
+```bash
+ai-spector index
+```
+
+Use `ai-spector index --force-graphify` if Graphify storage should rebuild even when file hashes are unchanged.
 - Optional: `/visualize-graph` for user review.
 - Suggest `/summary srs` only after graph ingest is complete.
 

package/scaffold/.cursor/commands/index.md

@@ -15,7 +15,9 @@ Rebuild **graph**, re-merge **knowledge** staging, refresh **Graphify storage**,
 - Graph validate fails due to stale structure
 - `.ai-spector/index/*.md` is out of date vs `docs/srs/` or `docs/basic-design/`
 
-**Does not replace `/analyze` for semantic extract** — `knowledge.json` is still produced by Graphify MCP during `/analyze`. This command re-merges existing knowledge and rebuilds structure/indexes.
+**Partial semantic refresh without `/analyze`:** After `/generate-srs`, index parses **UC/F/actor ids from markdown bodies** under `docs/srs/` and `docs/basic-design/` into the traceability graph, and runs **Graphify `update` on changed sources** (`docs/data-source`, `docs/srs`, `docs/basic-design`).
+
+**Still requires `/analyze` for:** full Graphify MCP extract → `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)
 
@@ -23,6 +25,23 @@ Rebuild **graph**, re-merge **knowledge** staging, refresh **Graphify storage**,
 ai-spector index
 ```
 
+After **`/generate-srs`** (recommended):
+
+```bash
+ai-spector index
+```
+
+Index steps (default): registry/bootstrap → knowledge merge → **SRS/docs body extract** → Graphify (changed paths only) → validate → doc indexes.
+
+Flags:
+
+| Flag | Effect |
+|------|--------|
+| `--force-graphify` | Re-index all Graphify sources even when content hash unchanged |
+| `--skip-doc-semantics` | Skip UC/F parsing from `docs/srs` and `docs/basic-design` |
+| `--skip-merge` | Skip `knowledge.json` merge |
+| `--skip-graphify` | Skip Graphify CLI entirely |
+
 On Graphify missing or CI without `uv`:
 
 ```bash