@spikedpunch/mast 0.1.0 → 0.3.0

package/dist/cli/serve.d.ts

@@ -1,3 +1,8 @@
 import type { Command } from 'commander';
-export declare function registerServeCommand(program: Command): void;
+import { type ServeOptions } from '../mcp/server.js';
+/**
+ * @param runServe Injected so the flag semantics below can be tested without
+ *   standing up a real stdio MCP server (§4.4). Production passes `serve`.
+ */
+export declare function registerServeCommand(program: Command, runServe?: (options: ServeOptions) => Promise<void>): void;
 //# sourceMappingURL=serve.d.ts.map

package/dist/cli/serve.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"serve.d.ts","sourceRoot":"","sources":["../../src/cli/serve.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEzC,OAAO,EAAS,KAAK,YAAY,EAAE,MAAM,kBAAkB,CAAC;AAE5D;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,OAAO,EAChB,QAAQ,GAAE,CAAC,OAAO,EAAE,YAAY,KAAK,OAAO,CAAC,IAAI,CAAS,GACzD,IAAI,CAyBN"}

package/dist/cli/serve.js

@@ -1,18 +1,28 @@
 import { resolveConfig } from '../store/config.js';
 import { serve } from '../mcp/server.js';
-export function registerServeCommand(program) {
+/**
+ * @param runServe Injected so the flag semantics below can be tested without
+ *   standing up a real stdio MCP server (§4.4). Production passes `serve`.
+ */
+export function registerServeCommand(program, runServe = serve) {
     program
         .command('serve')
         .description('Start the MCP server over stdio')
         .option('--state-dir <dir>', 'State directory')
         .option('--no-startup-reindex', 'Skip the startup staleness check (not recommended)')
-        .option('--watch', 'Watch source files and incrementally reindex on change (interactive use)')
+        // Declaration order is load-bearing: commander gives a boolean pair its
+        // default from whichever half is declared FIRST, so `--no-watch` must come
+        // before `--watch` for the default to be true. `--watch` is kept because
+        // existing MCP client configs pass it explicitly; it is now a no-op that
+        // selects the default. Pinned by cli/__tests__/serve-options.test.ts.
+        .option('--no-watch', 'Do not watch source files; rely on the startup reindex and explicit mast_reindex calls')
+        .option('--watch', 'Watch source files and incrementally reindex on change (the default)')
         .action(async (opts) => {
         const config = resolveConfig({ stateDirOverride: opts.stateDir });
-        await serve({
+        await runServe({
             config,
             noStartupReindex: !opts.startupReindex,
-            watch: opts.watch === true,
+            watch: opts.watch,
         });
     });
 }

package/dist/cli/serve.js.map

@@ -1 +1 @@
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+{"version":3,"file":"serve.js","sourceRoot":"","sources":["../../src/cli/serve.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AACnD,OAAO,EAAE,KAAK,EAAqB,MAAM,kBAAkB,CAAC;AAE5D;;;GAGG;AACH,MAAM,UAAU,oBAAoB,CAClC,OAAgB,EAChB,WAAqD,KAAK;IAE1D,OAAO;SACJ,OAAO,CAAC,OAAO,CAAC;SAChB,WAAW,CAAC,iCAAiC,CAAC;SAC9C,MAAM,CAAC,mBAAmB,EAAE,iBAAiB,CAAC;SAC9C,MAAM,CAAC,sBAAsB,EAAE,oDAAoD,CAAC;QACrF,wEAAwE;QACxE,2EAA2E;QAC3E,yEAAyE;QACzE,yEAAyE;QACzE,sEAAsE;SACrE,MAAM,CAAC,YAAY,EAAE,wFAAwF,CAAC;SAC9G,MAAM,CAAC,SAAS,EAAE,sEAAsE,CAAC;SACzF,MAAM,CAAC,KAAK,EAAE,IAId,EAAE,EAAE;QACH,MAAM,MAAM,GAAG,aAAa,CAAC,EAAE,gBAAgB,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;QAClE,MAAM,QAAQ,CAAC;YACb,MAAM;YACN,gBAAgB,EAAE,CAAC,IAAI,CAAC,cAAc;YACtC,KAAK,EAAE,IAAI,CAAC,KAAK;SAClB,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACP,CAAC"}

package/dist/cli/status.d.ts

@@ -1,6 +1,16 @@
 import type { Command } from 'commander';
+import type { StaleBreakdown } from '../ast/types.js';
 export interface StatusReport {
     readonly state_dir: string;
+    /**
+     * The tree this report was measured against.
+     *
+     * Reported because `state_dir` alone does not identify it, and the two are
+     * independently settable: a relative `--state-dir` resolves against the path
+     * argument, so it is entirely possible to read one project's index while
+     * asking about another project's files (D048).
+     */
+    readonly project_root: string;
     /** False when nothing has ever been indexed at `state_dir`. */
     readonly initialised: boolean;
     readonly schema_version: string;
@@ -9,6 +19,11 @@ export interface StatusReport {
     readonly chunk_count: number | null;
     /** `null` when there is no index — a stale count against nothing is meaningless. */
     readonly stale_files: number | null;
+    /**
+     * `stale_files` split into the three categories it sums. `null` on the same
+     * condition, and for the same reason.
+     */
+    readonly stale_breakdown: StaleBreakdown | null;
     readonly parse_errors: number | null;
     readonly write_errors: number | null;
     readonly index_fresh: boolean;

package/dist/cli/status.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"status.d.ts","sourceRoot":"","sources":["../../src/cli/status.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AAMtD,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B;;;;;;;OAOG;IACH,QAAQ,CAAC,YAAY,EAAE,MAAM,CAAC;IAC9B,+DAA+D;IAC/D,QAAQ,CAAC,WAAW,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,cAAc,EAAE,MAAM,CAAC;IAChC,QAAQ,CAAC,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IACrC,QAAQ,CAAC,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IACtC,QAAQ,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IACpC,oFAAoF;IACpF,QAAQ,CAAC,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IACpC;;;OAGG;IACH,QAAQ,CAAC,eAAe,EAAE,cAAc,GAAG,IAAI,CAAC;IAChD,QAAQ,CAAC,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IACrC,QAAQ,CAAC,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IACrC,QAAQ,CAAC,WAAW,EAAE,OAAO,CAAC;IAC9B,QAAQ,CAAC,eAAe,EAAE,MAAM,GAAG,IAAI,CAAC;IACxC,QAAQ,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAC3C;AAED;;;;;;;;;;;GAWG;AACH,wBAAsB,WAAW,CAC/B,OAAO,GAAE;IAAE,IAAI,CAAC,EAAE,MAAM,CAAC;IAAC,QAAQ,CAAC,EAAE,MAAM,CAAA;CAAO,GACjD,OAAO,CAAC,YAAY,CAAC,CAuDvB;AAED,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAqE5D"}

package/dist/cli/status.js

@@ -20,12 +20,14 @@ export async function buildStatus(options = {}) {
     if (meta === null) {
         return {
             state_dir: config.resolved_state_dir,
+            project_root: config.resolved_project_root,
             initialised: false,
             schema_version: CURRENT_SCHEMA_VERSION,
             last_indexed: null,
             indexed_files: null,
             chunk_count: null,
             stale_files: null,
+            stale_breakdown: null,
             parse_errors: null,
             write_errors: null,
             index_fresh: false,
@@ -37,26 +39,32 @@ export async function buildStatus(options = {}) {
     // above, because the `meta === null` branch has already returned for a state
     // dir that was never indexed.
     const db = openDatabase(config.resolved_state_dir);
-    let staleCount;
+    let freshness;
     try {
-        staleCount = (await measureFreshness(config, db)).total;
+        freshness = await measureFreshness(config, db);
     }
     finally {
         await db.destroy();
     }
     return {
         state_dir: config.resolved_state_dir,
+        project_root: config.resolved_project_root,
         initialised: true,
         // From the binary, never from index.json — see StatusResult.schema_version.
         schema_version: CURRENT_SCHEMA_VERSION,
         last_indexed: meta.last_indexed ?? null,
         indexed_files: meta.file_count ?? 0,
         chunk_count: meta.chunk_count ?? 0,
-        stale_files: staleCount,
+        stale_files: freshness.total,
+        stale_breakdown: {
+            changed: freshness.stale,
+            unindexed: freshness.unindexed,
+            deleted: freshness.deleted,
+        },
         parse_errors: meta.parse_errors ?? 0,
         write_errors: meta.write_errors ?? 0,
-        index_fresh: staleCount === 0,
-        freshness_cause: freshnessCause(staleCount),
+        index_fresh: freshness.total === 0,
+        freshness_cause: freshnessCause(freshness),
         seed_commit: meta.seed_commit,
     };
 }
@@ -89,18 +97,36 @@ export function registerStatusCommand(program) {
         const ago = status.last_indexed != null
             ? ` (${formatAge(new Date(status.last_indexed))} ago)`
             : '';
+        // The split is printed inline rather than on its own line: `stale_files`
+        // names one of the three things it counts, and the total alone has been
+        // read as "3391 files changed" when it was one changed file and 3390
+        // paths belonging to another tree (D049).
+        const b = status.stale_breakdown;
+        const split = b !== null && (status.stale_files ?? 0) > 0
+            ? `  (changed ${String(b.changed)}, unindexed ${String(b.unindexed)}, deleted ${String(b.deleted)})`
+            : '';
         process.stdout.write([
             `state_dir:      ${status.state_dir}`,
+            `project_root:   ${status.project_root}`,
             `schema_version: ${status.schema_version}`,
             `last_indexed:   ${status.last_indexed ?? 'never'}${ago}`,
             `indexed_files:  ${String(status.indexed_files)}`,
             `chunk_count:    ${String(status.chunk_count)}`,
-            `stale_files:    ${String(status.stale_files)}`,
+            `stale_files:    ${String(status.stale_files)}${split}`,
             `parse_errors:   ${String(status.parse_errors)}`,
             `write_errors:   ${String(status.write_errors)}`,
             `index_fresh:    ${String(status.index_fresh)}`,
             `freshness_cause: ${status.freshness_cause ?? 'none'}`,
             ...(status.seed_commit != null ? [`seed_commit:    ${status.seed_commit}`] : []),
+            ...(status.freshness_cause === 'root_mismatch' ? [
+                '',
+                `! This index does not describe the tree at ${status.project_root}.`,
+                '  Most files here are unknown to it, and most files it lists are not here —',
+                '  it was built for a different project root, so reindexing will not move',
+                '  these numbers. Check the path argument and --state-dir: a relative',
+                '  --state-dir resolves against the path argument, not the shell\'s',
+                '  working directory.',
+            ] : []),
         ].join('\n') + '\n');
     });
 }

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package/dist/indexer/freshness.d.ts

@@ -36,6 +36,16 @@ export interface IndexFreshness {
     readonly deleted: number;
     /** `stale + unindexed + deleted` — what both surfaces report as `stale_files`. */
     readonly total: number;
+    /**
+     * Indexable files this walk found, whatever their index state — the
+     * denominator the three counts above are drawn against.
+     *
+     * Carried so a caller can tell "some of this tree is unindexed" from "none of
+     * this tree is indexed", which is the difference between a stale index and an
+     * index built for a different project root (D048). Without it `unindexed` is
+     * a bare count with nothing to compare it to.
+     */
+    readonly walked: number;
 }
 /**
  * Measure the index against the working tree.

package/dist/indexer/freshness.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"freshness.d.ts","sourceRoot":"","sources":["../../src/indexer/freshness.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAIH,OAAO,KAAK,EAAE,EAAE,EAAE,MAAM,gBAAgB,CAAC;AACzC,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAGzD,MAAM,WAAW,cAAc;IAC7B,yEAAyE;IACzE,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,qEAAqE;IACrE,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,6CAA6C;IAC7C,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,kFAAkF;IAClF,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;CACxB;AAED;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CAAC,MAAM,EAAE,cAAc,EAAE,EAAE,EAAE,EAAE,GAAG,OAAO,CAAC,cAAc,CAAC,CAiC9F"}
+{"version":3,"file":"freshness.d.ts","sourceRoot":"","sources":["../../src/indexer/freshness.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAIH,OAAO,KAAK,EAAE,EAAE,EAAE,MAAM,gBAAgB,CAAC;AACzC,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAGzD,MAAM,WAAW,cAAc;IAC7B,yEAAyE;IACzE,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,qEAAqE;IACrE,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,6CAA6C;IAC7C,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,kFAAkF;IAClF,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB;;;;;;;;OAQG;IACH,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;CACzB;AAED;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CAAC,MAAM,EAAE,cAAc,EAAE,EAAE,EAAE,EAAE,GAAG,OAAO,CAAC,cAAc,CAAC,CAuC9F"}

package/dist/indexer/freshness.js

@@ -67,6 +67,12 @@ export async function measureFreshness(config, db) {
     for (const path of indexed.keys())
         if (!onDisk.has(path))
             gone.add(path);
-    return { stale, unindexed, deleted: gone.size, total: stale + unindexed + gone.size };
+    return {
+        stale,
+        unindexed,
+        deleted: gone.size,
+        total: stale + unindexed + gone.size,
+        walked: onDisk.size,
+    };
 }
 //# sourceMappingURL=freshness.js.map

package/dist/indexer/freshness.js.map

@@ -1 +1 @@
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package/dist/indexer/import-resolver.js

@@ -90,24 +90,36 @@ function buildResolver(projectRoot) {
     };
     /** Resolve a base path (possibly without extension) to a real indexed file. */
     const probe = (base, ctx) => {
-        // NodeNext source-first precedence: when the specifier carries a compiled
-        // JS extension (`./x.js`), prefer the TypeScript source (`x.ts`) that would
-        // emit it, ahead of any literal `x.js` on disk (see JS_TO_TS_EXTS).
-        for (const [jsExt, tsExts] of JS_TO_TS_EXTS) {
-            if (base.endsWith(jsExt)) {
-                const stem = base.slice(0, -jsExt.length);
-                for (const tsExt of tsExts) {
-                    if (isFile(stem + tsExt))
-                        return toRel(stem + tsExt, ctx);
+        // D047: a specifier written with a trailing slash names a DIRECTORY and
+        // nothing else — `require.resolve('./routes/')` throws MODULE_NOT_FOUND
+        // when only `routes.ts` exists. `base` cannot carry that intent, because
+        // `path.resolve`/`join` normalise the slash away before we are called, so
+        // it is read off the specifier the caller preserved on `ctx`. Without this
+        // the sibling probes below win over the directory the author explicitly
+        // asked for: `Routes.ts` importing `./routes/` resolved to *itself* on a
+        // case-insensitive filesystem, and `routes/index.ts` — which had a live
+        // importer — was recorded with none.
+        const directoryOnly = ctx.specifier.endsWith('/');
+        if (!directoryOnly) {
+            // NodeNext source-first precedence: when the specifier carries a compiled
+            // JS extension (`./x.js`), prefer the TypeScript source (`x.ts`) that would
+            // emit it, ahead of any literal `x.js` on disk (see JS_TO_TS_EXTS).
+            for (const [jsExt, tsExts] of JS_TO_TS_EXTS) {
+                if (base.endsWith(jsExt)) {
+                    const stem = base.slice(0, -jsExt.length);
+                    for (const tsExt of tsExts) {
+                        if (isFile(stem + tsExt))
+                            return toRel(stem + tsExt, ctx);
+                    }
+                    break; // a base ends in at most one of these extensions
                 }
-                break; // a base ends in at most one of these extensions
             }
-        }
-        if (isFile(base))
-            return toRel(base, ctx);
-        for (const ext of CANDIDATE_EXTS) {
-            if (isFile(base + ext))
-                return toRel(base + ext, ctx);
+            if (isFile(base))
+                return toRel(base, ctx);
+            for (const ext of CANDIDATE_EXTS) {
+                if (isFile(base + ext))
+                    return toRel(base + ext, ctx);
+            }
         }
         for (const ext of CANDIDATE_EXTS) {
             const idx = join(base, `index${ext}`);

package/dist/indexer/import-resolver.js.map

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package/dist/indexer/index.d.ts

@@ -6,6 +6,7 @@ import type { WriteSpansMs } from '../graph/populate.js';
 import { extractFile } from '../ast/extract.js';
 import { type MiscasedImportReport } from './import-resolver.js';
 import type { IndexMeta, FreshnessCause } from '../ast/types.js';
+import type { IndexFreshness } from './freshness.js';
 export interface IndexResult {
     readonly filesIndexed: number;
     readonly filesSkipped: number;
@@ -226,15 +227,49 @@ export interface IndexOptions {
  */
 export declare function runIndex(config: ResolvedConfig, options: IndexOptions): Promise<IndexResult>;
 /**
- * Derive the `freshness_cause` discriminator (§9 mast_status) from the stale
- * file count. Stage 7.2 (IMPLEMENTATION_PLAN.md "Stage 7: Vector-store
+ * Derive the `freshness_cause` discriminator (§9 mast_status) from the measured
+ * freshness. Stage 7.2 (IMPLEMENTATION_PLAN.md "Stage 7: Vector-store
  * deletion") dropped the second parameter this used to take
  * (`pendingEmbeddings`) along with the `'embedding_backlog'`/`'both'` cases —
  * the Phase 2 embedder that could produce a backlog distinct from Phase 1
  * staleness was excised in Stage 7.1, so a two-cause signature asserted a
  * distinction the code could no longer draw.
+ *
+ * It took the bare total from then until 2026-09-01 (D049), which asserted the
+ * opposite error: `'phase1_stale'` for any non-zero count, including counts
+ * with no stale file in them at all. It now takes the whole measurement,
+ * because every distinction it draws is one `measureFreshness` already counted.
+ *
+ * `root_mismatch` is tested first and is the only compound condition. Let
+ * `matched` be the files on disk the index actually knows (`walked -
+ * unindexed`); the index describes a different tree when it disagrees with this
+ * one in *both* directions more than it agrees in either — more unknown files
+ * here than known ones, and more files listed that are absent than known ones.
+ *
+ * Both halves are load-bearing, and each excludes a different neighbour:
+ * dropping the `unindexed` half would call a mass deletion a root mismatch
+ * (many `deleted`, but every remaining file still matches); dropping the
+ * `deleted` half would call a never-indexed project one (everything unknown,
+ * but the index claims no files elsewhere).
+ *
+ * Stated as strict majorities against `matched` rather than as a ratio against
+ * a tuned constant, and deliberately NOT as `unindexed === walked`: that was the
+ * first form, and on the 1822-file index this was written for it did not fire,
+ * because exactly one walked path coincidentally matched an indexed one and
+ * `1569 === 1570` is false. A guard that a single accidental collision defeats
+ * is the shape this ledger calls S-02.
+ *
+ * It is decided from counted content rather than by comparing the project root
+ * against the one in the persisted state config: that path is recorded from a
+ * previous process and is meaningless under the shared-volume mounts
+ * `pickStateConfigCustomization` exists to survive.
+ *
+ * The remaining three are ordered by what a caller should do about them, not by
+ * size: `phase1_stale` first because it is the one JIT re-parse silently
+ * corrects on read, so it is the least alarming reading of a mixed count. The
+ * exact split always travels beside it in `stale_breakdown`.
  */
-export declare function freshnessCause(staleFiles: number): FreshnessCause;
+export declare function freshnessCause(freshness: IndexFreshness): FreshnessCause;
 /**
  * Load `index.json` from the state directory, or return null if absent.
  *

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

@@ -1 +1 @@
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package/dist/indexer/index.js

@@ -528,16 +528,59 @@ function symbolSignature(symbols) {
 // Freshness diagnostics (mast_status, `mast status`)
 // ---------------------------------------------------------------------------
 /**
- * Derive the `freshness_cause` discriminator (§9 mast_status) from the stale
- * file count. Stage 7.2 (IMPLEMENTATION_PLAN.md "Stage 7: Vector-store
+ * Derive the `freshness_cause` discriminator (§9 mast_status) from the measured
+ * freshness. Stage 7.2 (IMPLEMENTATION_PLAN.md "Stage 7: Vector-store
  * deletion") dropped the second parameter this used to take
  * (`pendingEmbeddings`) along with the `'embedding_backlog'`/`'both'` cases —
  * the Phase 2 embedder that could produce a backlog distinct from Phase 1
  * staleness was excised in Stage 7.1, so a two-cause signature asserted a
  * distinction the code could no longer draw.
+ *
+ * It took the bare total from then until 2026-09-01 (D049), which asserted the
+ * opposite error: `'phase1_stale'` for any non-zero count, including counts
+ * with no stale file in them at all. It now takes the whole measurement,
+ * because every distinction it draws is one `measureFreshness` already counted.
+ *
+ * `root_mismatch` is tested first and is the only compound condition. Let
+ * `matched` be the files on disk the index actually knows (`walked -
+ * unindexed`); the index describes a different tree when it disagrees with this
+ * one in *both* directions more than it agrees in either — more unknown files
+ * here than known ones, and more files listed that are absent than known ones.
+ *
+ * Both halves are load-bearing, and each excludes a different neighbour:
+ * dropping the `unindexed` half would call a mass deletion a root mismatch
+ * (many `deleted`, but every remaining file still matches); dropping the
+ * `deleted` half would call a never-indexed project one (everything unknown,
+ * but the index claims no files elsewhere).
+ *
+ * Stated as strict majorities against `matched` rather than as a ratio against
+ * a tuned constant, and deliberately NOT as `unindexed === walked`: that was the
+ * first form, and on the 1822-file index this was written for it did not fire,
+ * because exactly one walked path coincidentally matched an indexed one and
+ * `1569 === 1570` is false. A guard that a single accidental collision defeats
+ * is the shape this ledger calls S-02.
+ *
+ * It is decided from counted content rather than by comparing the project root
+ * against the one in the persisted state config: that path is recorded from a
+ * previous process and is meaningless under the shared-volume mounts
+ * `pickStateConfigCustomization` exists to survive.
+ *
+ * The remaining three are ordered by what a caller should do about them, not by
+ * size: `phase1_stale` first because it is the one JIT re-parse silently
+ * corrects on read, so it is the least alarming reading of a mixed count. The
+ * exact split always travels beside it in `stale_breakdown`.
  */
-export function freshnessCause(staleFiles) {
-    return staleFiles > 0 ? 'phase1_stale' : null;
+export function freshnessCause(freshness) {
+    if (freshness.total === 0)
+        return null;
+    const matched = freshness.walked - freshness.unindexed;
+    if (freshness.unindexed > matched && freshness.deleted > matched)
+        return 'root_mismatch';
+    if (freshness.stale > 0)
+        return 'phase1_stale';
+    if (freshness.unindexed > 0)
+        return 'unindexed_files';
+    return 'deleted_files';
 }
 /**
  * Load `index.json` from the state directory, or return null if absent.

package/dist/indexer/index.js.map

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package/dist/indexer/watcher.d.ts

@@ -68,6 +68,22 @@ export interface StartWatchModeOptions {
     /** One incremental Phase 1 + embed run; supplied by the serve lifecycle. */
     readonly runBatch: (paths: readonly string[]) => Promise<void>;
     readonly onWarn: (message: string) => void;
+    /**
+     * Called once, when chokidar has finished its initial scan and is actually
+     * delivering events.
+     *
+     * The watcher starts AFTER `serve` accepts MCP connections, and it is
+     * constructed with `ignoreInitial: true` — correct, since the startup ladder
+     * has already indexed the tree, but it means a file created before the scan
+     * finishes is treated as pre-existing and fires no event at all. Without this
+     * callback nothing outside the process could tell that window apart from
+     * "watching, nothing has changed" or from "the watcher failed to start": the
+     * EMFILE path warns, and the success path was silent, so silence meant three
+     * different things (D061).
+     *
+     * Optional. A caller that does not want the signal still gets a watcher.
+     */
+    readonly onReady?: () => void;
     /** Override for tests; production default 500ms. */
     readonly debounceMs?: number;
 }

package/dist/indexer/watcher.d.ts.map

@@ -1 +1 @@
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