@vizalice/codegraph 1.5.0 → 1.6.1

package/dist/search/identifier-segments.js.map

@@ -1 +1 @@
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package/dist/search/query-paths.d.ts

@@ -0,0 +1,57 @@
+/**
+ * File-path recognition for explore queries.
+ *
+ * Agents routinely name files by path in a `codegraph_explore` query —
+ * "the scroll logic in src/routes/m/projects/[id]/runs/[runId]/+page.svelte" —
+ * and until this module existed those spans were SHREDDED by the downstream
+ * tokenizers instead of being read as file references:
+ *
+ *   - the named-symbol seeder splits on `[\s,()[\]]+`, so SvelteKit/Next
+ *     bracketed segments (`[id]`, `[runId]`) and route groups (`(protected)`)
+ *     exploded the path into fragments; the identifier-shaped survivors
+ *     (`runId`, `scope`) then seeded as "symbols the agent named" and
+ *     headlined the blast radius;
+ *   - FTS saw the fragments (`page`, `chat`, `runs`) and admitted every
+ *     sibling `+page.svelte` in the repo, which ate the output envelope and
+ *     truncated the files the agent actually asked for.
+ *
+ * `extractQueryPaths` finds path-like spans — slashed paths, dotted basenames,
+ * and extension-less kebab basenames (`background-image-table`, the spelling
+ * import paths and prose actually use) — resolves them against the INDEXED
+ * file list (resolution IS the detector — `and/or`, `gen_server:call/2`,
+ * `non-blocking` and other path-shaped non-paths match nothing and are left
+ * alone), and returns the matches as pinned files plus the query with those
+ * spans removed.
+ * Callers treat pinned files as first-class: guaranteed admission, top rank,
+ * funded first. Pure string work — no DB, no fs — so it is trivially testable
+ * and safe inside the query-pool workers.
+ */
+export interface QueryPathExtraction {
+    /** The query with resolved/clearly-path spans removed, whitespace-joined. */
+    strippedQuery: string;
+    /** Indexed file paths the query named, appearance-ordered, deduped. */
+    pinnedFiles: string[];
+    /**
+     * Spans that are unambiguously path-shaped but resolved to nothing (stale
+     * path, unindexed file) or to too many files (bare `+page.svelte`). Stripped
+     * from the query — their fragments could only mint junk matches — and
+     * surfaced to the agent so the miss is visible instead of silent.
+     */
+    unresolvedPathSpans: string[];
+}
+/**
+ * Cheap pre-gate so callers only fetch the indexed file list when the query
+ * could possibly contain a path: a slash, a dot-extension-shaped tail
+ * (`chat-manager.ts`), or a hyphen-joined word (`background-image-table` —
+ * kebab files are named WITHOUT their extension more often than with, so the
+ * shape must open the gate on its own). Extensions cap at 8 chars, which
+ * keeps `Class.method` spans (`app.isPackaged`) from qualifying; the kebab
+ * alternative requires clean non-word boundaries, which keeps `--flags` and
+ * snake_case-with-a-dash hybrids from firing it.
+ */
+export declare function queryMightContainPaths(query: string): boolean;
+export declare function extractQueryPaths(query: string, indexedPaths: readonly string[], opts?: {
+    maxPins?: number;
+    maxMatchesPerSpan?: number;
+}): QueryPathExtraction;
+//# sourceMappingURL=query-paths.d.ts.map

package/dist/search/query-paths.d.ts.map

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package/dist/search/query-paths.js

@@ -0,0 +1,298 @@
+"use strict";
+/**
+ * File-path recognition for explore queries.
+ *
+ * Agents routinely name files by path in a `codegraph_explore` query —
+ * "the scroll logic in src/routes/m/projects/[id]/runs/[runId]/+page.svelte" —
+ * and until this module existed those spans were SHREDDED by the downstream
+ * tokenizers instead of being read as file references:
+ *
+ *   - the named-symbol seeder splits on `[\s,()[\]]+`, so SvelteKit/Next
+ *     bracketed segments (`[id]`, `[runId]`) and route groups (`(protected)`)
+ *     exploded the path into fragments; the identifier-shaped survivors
+ *     (`runId`, `scope`) then seeded as "symbols the agent named" and
+ *     headlined the blast radius;
+ *   - FTS saw the fragments (`page`, `chat`, `runs`) and admitted every
+ *     sibling `+page.svelte` in the repo, which ate the output envelope and
+ *     truncated the files the agent actually asked for.
+ *
+ * `extractQueryPaths` finds path-like spans — slashed paths, dotted basenames,
+ * and extension-less kebab basenames (`background-image-table`, the spelling
+ * import paths and prose actually use) — resolves them against the INDEXED
+ * file list (resolution IS the detector — `and/or`, `gen_server:call/2`,
+ * `non-blocking` and other path-shaped non-paths match nothing and are left
+ * alone), and returns the matches as pinned files plus the query with those
+ * spans removed.
+ * Callers treat pinned files as first-class: guaranteed admission, top rank,
+ * funded first. Pure string work — no DB, no fs — so it is trivially testable
+ * and safe inside the query-pool workers.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.queryMightContainPaths = queryMightContainPaths;
+exports.extractQueryPaths = extractQueryPaths;
+/**
+ * Cheap pre-gate so callers only fetch the indexed file list when the query
+ * could possibly contain a path: a slash, a dot-extension-shaped tail
+ * (`chat-manager.ts`), or a hyphen-joined word (`background-image-table` —
+ * kebab files are named WITHOUT their extension more often than with, so the
+ * shape must open the gate on its own). Extensions cap at 8 chars, which
+ * keeps `Class.method` spans (`app.isPackaged`) from qualifying; the kebab
+ * alternative requires clean non-word boundaries, which keeps `--flags` and
+ * snake_case-with-a-dash hybrids from firing it.
+ */
+function queryMightContainPaths(query) {
+    return /[/\\]/.test(query)
+        || /\.[A-Za-z][A-Za-z0-9]{0,7}(?=[\s,;:)\]'"`]|$)/.test(query)
+        || /(?:^|[^-\w])[A-Za-z0-9]+(?:-[A-Za-z0-9]+)+(?=[^-\w]|$)/.test(query);
+}
+/**
+ * Longest span→suffix walk tried per span. 8 covers an absolute macOS path
+ * (`/Users/<user>/dev/<repo>/…`) over a deeply nested repo-relative file;
+ * deeper prefixes buy nothing.
+ */
+const MAX_SUFFIX_TRIES = 8;
+/** Spans examined per query — a prose sentence is not 50 paths. */
+const MAX_CANDIDATE_SPANS = 8;
+/** `name.ext` shape with a plausible source extension (no slash required). */
+const DOTTED_BASENAME = /^[^\s/\\]+\.[A-Za-z][A-Za-z0-9]{0,7}$/;
+/**
+ * Extension-less kebab basename (`background-image-table`). Hyphens are
+ * illegal in identifiers, so consuming these tokens can never steal one from
+ * the named-symbol seeder; ≥2 segments keeps single words out.
+ */
+const KEBAB_BASENAME = /^[A-Za-z0-9]+(?:-[A-Za-z0-9]+)+$/;
+/** A basename's last dot-extension, same shape DOTTED_BASENAME accepts. */
+const LAST_EXTENSION = /\.[A-Za-z][A-Za-z0-9]{0,7}$/;
+/**
+ * Lowercased basename stems of the hyphen-named indexed files, stem → paths.
+ * A stem drops only the LAST extension (`a-b.module.scss` → `a-b.module`), so
+ * a bare kebab token can't accidentally pin a same-named stylesheet or
+ * `.d.ts` sibling of the source file it names; an extension-less basename
+ * (`pre-commit`) is its own stem. Hyphen-free basenames are skipped — a
+ * KEBAB_BASENAME token can never equal one, and the filter keeps the map
+ * near-empty in repos that don't name files this way.
+ */
+function buildBasenameStems(indexedPaths) {
+    const stems = new Map();
+    for (const p of indexedPaths) {
+        const basename = p.slice(Math.max(p.lastIndexOf('/'), p.lastIndexOf('\\')) + 1);
+        if (!basename.includes('-'))
+            continue;
+        const stem = basename.replace(LAST_EXTENSION, '').toLowerCase();
+        if (!stem)
+            continue;
+        const existing = stems.get(stem);
+        if (existing)
+            existing.push(p);
+        else
+            stems.set(stem, [p]);
+    }
+    return stems;
+}
+/**
+ * Strip prose punctuation wrapped around a token without eating punctuation
+ * that is PART of the path: quotes/backticks always strip; a trailing `)`/`]`
+ * strips only when the token has no matching opener (so `(protected)` and
+ * `[id]` segments survive, while "…(see src/foo.ts)" loses its parenthesis);
+ * a leading `(`/`[` mirrors that. Trailing sentence punctuation strips last,
+ * so "src/foo.ts." resolves.
+ */
+function stripWrapping(token) {
+    let s = token;
+    for (;;) {
+        const first = s[0];
+        if (!first)
+            break;
+        if ('\'"`<'.includes(first)) {
+            s = s.slice(1);
+            continue;
+        }
+        if (first === '(' && !s.includes(')')) {
+            s = s.slice(1);
+            continue;
+        }
+        if (first === '[' && !s.includes(']')) {
+            s = s.slice(1);
+            continue;
+        }
+        if (first === '{' && !s.includes('}')) {
+            s = s.slice(1);
+            continue;
+        }
+        break;
+    }
+    for (;;) {
+        const last = s[s.length - 1];
+        if (!last)
+            break;
+        if ('\'"`>.,;!?'.includes(last)) {
+            s = s.slice(0, -1);
+            continue;
+        }
+        if (last === ')' && !s.includes('(')) {
+            s = s.slice(0, -1);
+            continue;
+        }
+        if (last === ']' && !s.includes('[')) {
+            s = s.slice(0, -1);
+            continue;
+        }
+        if (last === '}' && !s.includes('{')) {
+            s = s.slice(0, -1);
+            continue;
+        }
+        break;
+    }
+    // Line references ride along in agent-written paths: `foo.ts:123`,
+    // `foo.ts:12-40`, `foo.ts#L88`. The file is what gets pinned.
+    s = s.replace(/(?::\d+(?:-\d+)?|#L\d+(?:-L?\d+)?)$/, '');
+    return s;
+}
+/** Normalize a span into the repo-relative shape the files table stores. */
+function normalizeSpan(span) {
+    return span
+        .replace(/\\/g, '/')
+        .replace(/^(?:\.\/)+/, '')
+        .replace(/\/{2,}/g, '/')
+        .replace(/\/+$/, '');
+}
+/** Path-shaped beyond doubt: ≥2 segments and a dot-extension on the last. */
+function isClearlyPathShaped(normalized) {
+    const slash = normalized.lastIndexOf('/');
+    if (slash <= 0)
+        return false;
+    return DOTTED_BASENAME.test(normalized.slice(slash + 1));
+}
+/**
+ * Resolve one normalized span against the indexed paths: exact match first,
+ * then segment-aligned suffix matches, dropping leading segments one at a
+ * time (so an absolute path, or one prefixed with the repo directory name,
+ * still lands on the indexed repo-relative file). Suffixes only get shorter —
+ * and therefore only match MORE — so the walk stops at the first suffix that
+ * matches anything: within budget it resolves, over budget it is ambiguous.
+ */
+function resolveSpan(normalizedLower, lowerToOriginal, maxMatches) {
+    const exact = lowerToOriginal.get(normalizedLower);
+    if (exact)
+        return { matches: [exact], ambiguous: false };
+    const segments = normalizedLower.split('/').filter(Boolean);
+    const tries = Math.min(segments.length, MAX_SUFFIX_TRIES);
+    for (let drop = 0; drop < tries; drop++) {
+        const suffix = segments.slice(drop).join('/');
+        if (!suffix)
+            break;
+        const withSlash = '/' + suffix;
+        const matches = [];
+        for (const [lower, original] of lowerToOriginal) {
+            if (lower === suffix || lower.endsWith(withSlash)) {
+                matches.push(original);
+                if (matches.length > maxMatches)
+                    return { matches: [], ambiguous: true };
+            }
+        }
+        if (matches.length > 0)
+            return { matches, ambiguous: false };
+    }
+    return { matches: [], ambiguous: false };
+}
+function extractQueryPaths(query, indexedPaths, opts = {}) {
+    const maxPins = Math.max(1, opts.maxPins ?? 8);
+    const maxMatchesPerSpan = Math.max(1, opts.maxMatchesPerSpan ?? 3);
+    const passthrough = {
+        strippedQuery: query,
+        pinnedFiles: [],
+        unresolvedPathSpans: [],
+    };
+    if (!query.trim() || indexedPaths.length === 0)
+        return passthrough;
+    // Lowercase view of the index, built once per call. Last writer wins on a
+    // case-colliding pair, which is the existing file-view behavior too.
+    const lowerToOriginal = new Map();
+    for (const p of indexedPaths)
+        lowerToOriginal.set(p.toLowerCase(), p);
+    const tokens = query.split(/\s+/).filter(Boolean);
+    const consumed = new Set();
+    const pinned = [];
+    const pinnedSeen = new Set();
+    const unresolved = [];
+    let candidatesExamined = 0;
+    for (let i = 0; i < tokens.length; i++) {
+        if (pinned.length >= maxPins)
+            break;
+        if (candidatesExamined >= MAX_CANDIDATE_SPANS)
+            break;
+        const stripped = stripWrapping(tokens[i]);
+        if (stripped.length < 4)
+            continue;
+        const hasSlash = /[/\\]/.test(stripped);
+        if (!hasSlash && !DOTTED_BASENAME.test(stripped))
+            continue;
+        const normalized = normalizeSpan(stripped);
+        if (!normalized)
+            continue;
+        candidatesExamined++;
+        const { matches, ambiguous } = resolveSpan(normalized.toLowerCase(), lowerToOriginal, maxMatchesPerSpan);
+        if (matches.length > 0) {
+            consumed.add(i);
+            for (const m of matches) {
+                if (pinnedSeen.has(m) || pinned.length >= maxPins)
+                    continue;
+                pinnedSeen.add(m);
+                pinned.push(m);
+            }
+        }
+        else if (ambiguous || isClearlyPathShaped(normalized)) {
+            // A real path that didn't resolve to a usable set. Keeping it in the
+            // query is strictly worse — its fragments are what minted the junk
+            // matches this module exists to stop — so strip it and say so.
+            consumed.add(i);
+            if (unresolved.length < 4)
+                unresolved.push(normalized);
+        }
+        // Anything else (`and/or`, `call/2`, `foo.Bar`) is not a path reference:
+        // leave the token for the normal matching pipeline.
+    }
+    // Second pass — extension-less kebab basenames. `background-image-table`
+    // opens no door above (no slash, no dotted tail), the hyphens disqualify it
+    // from the named-symbol seeder downstream, and FTS shreds it into the most
+    // common words in a kebab-cased repo (`background`, `image`, `table`) —
+    // which admit look-alike SIBLINGS that crowd out the named file. Resolution
+    // stays the detector: a token pins only when its whole lowercased form is
+    // the stem of an indexed basename. Two deliberate asymmetries vs the first
+    // pass: prose that resolves to nothing (`non-blocking`, `cross-call`) is
+    // LEFT IN the query — unlike a slashed span it may be legitimate wording,
+    // so it keeps feeding FTS and is not reported as an unresolved path — and a
+    // stem hotter than maxMatchesPerSpan is likewise left alone (pinning half a
+    // monorepo off one hot name trades precision the wrong way; a directory
+    // segment, which the first pass handles, disambiguates). Runs after the
+    // slashed/dotted pass so explicit paths win the shared maxPins budget, and
+    // examines every remaining token: lookups are O(1) map hits, so the
+    // scan-cost rationale behind MAX_CANDIDATE_SPANS doesn't apply.
+    let basenameStems = null;
+    for (let i = 0; i < tokens.length && pinned.length < maxPins; i++) {
+        if (consumed.has(i))
+            continue;
+        const stripped = stripWrapping(tokens[i]);
+        if (stripped.length < 4 || !KEBAB_BASENAME.test(stripped))
+            continue;
+        basenameStems ??= buildBasenameStems(indexedPaths);
+        const matches = basenameStems.get(stripped.toLowerCase());
+        if (!matches || matches.length > maxMatchesPerSpan)
+            continue;
+        consumed.add(i);
+        for (const m of matches) {
+            if (pinnedSeen.has(m) || pinned.length >= maxPins)
+                continue;
+            pinnedSeen.add(m);
+            pinned.push(m);
+        }
+    }
+    if (consumed.size === 0)
+        return passthrough;
+    return {
+        strippedQuery: tokens.filter((_, i) => !consumed.has(i)).join(' '),
+        pinnedFiles: pinned,
+        unresolvedPathSpans: unresolved,
+    };
+}
+//# sourceMappingURL=query-paths.js.map

package/dist/search/query-paths.js.map

@@ -0,0 +1 @@
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package/dist/search/query-utils.d.ts

@@ -50,7 +50,7 @@ export declare function extractSearchTerms(query: string, options?: {
  * Score path relevance to a query
  * Higher score = more relevant path
  */
-export declare function scorePathRelevance(filePath: string, query: string, projectNameTokens?: Set<string>): number;
+export declare function scorePathRelevance(filePath: string, query: string, projectNameTokens?: Set<string>, isDeprioritized?: boolean): number;
 /**
  * Check if a file path looks like a test file
  */

package/dist/search/query-utils.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"query-utils.d.ts","sourceRoot":"","sources":["../../src/search/query-utils.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAEhC,6EAA6E;AAC7E,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAEtD;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,uBAAuB,CAAC,WAAW,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC,CAyBxE;AAED;;;GAGG;AACH,eAAO,MAAM,UAAU,aAkBrB,CAAC;AAEH;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,EAAE,CAyDtD;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,MAAM,EAAE,CA2DzF;AAED;;;GAGG;AACH,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,MAAM,EACb,iBAAiB,CAAC,EAAE,GAAG,CAAC,MAAM,CAAC,EAC/B,eAAe,CAAC,EAAE,OAAO,GACxB,MAAM,CA2DR;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAuCpD;AAmBD;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CAuCtE;AAED;;;GAGG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,GAAG,MAAM,CA2BpD;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAQ9D"}

package/dist/search/query-utils.js

@@ -244,7 +244,7 @@ function extractSearchTerms(query, options) {
  * Score path relevance to a query
  * Higher score = more relevant path
  */
-function scorePathRelevance(filePath, query, projectNameTokens) {
+function scorePathRelevance(filePath, query, projectNameTokens, isDeprioritized) {
     const pathLower = filePath.toLowerCase();
     const fileName = path.basename(filePath).toLowerCase();
     const dirName = path.dirname(filePath).toLowerCase();
@@ -286,10 +286,19 @@ function scorePathRelevance(filePath, query, projectNameTokens) {
         else if (subtokens.some((t) => pathLower.includes(t)))
             score += 3;
     }
-    // Deprioritize test files unless the query is explicitly about tests
+    // Deprioritize test files unless the query is explicitly about tests, and
+    // apply the same -15 to a path the project declared peripheral (#982).
+    //
+    // Two deliberate asymmetries, both pinned by tests:
+    //  - the built-in test/fixture penalty is waived for a test-y query, because
+    //    the tool inferred that classification; a `deprioritize` pattern is a
+    //    standing statement by the project, so it is NOT waived. The name-bonus
+    //    damping at the call site is what keeps such a tree findable.
+    //  - a path that is both is docked ONCE, not twice.
     const queryLower = query.toLowerCase();
     const isTestQuery = queryLower.includes('test') || queryLower.includes('spec');
-    if (!isTestQuery && isTestFile(filePath)) {
+    const offTarget = (!isTestQuery && isTestFile(filePath)) || isDeprioritized === true;
+    if (offTarget) {
         score -= 15;
     }
     return score;

package/dist/search/query-utils.js.map

@@ -1 +1 @@
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package/dist/sync/watcher.d.ts

@@ -247,6 +247,28 @@ export declare class FileWatcher {
      * — it drops node_modules/dist/.git churn before any sync is scheduled.
      */
     private handleChange;
+    /**
+     * A scope-defining file changed (`codegraph.json`, a `.gitignore`): rebuild
+     * the ignore matcher and make the next sync a FULL reconcile (#1590).
+     *
+     * The matcher used to be built once in `start()` and kept for the watcher's
+     * lifetime — in a long-lived MCP daemon that meant a `codegraph.json`
+     * created or edited after startup was invisible to the live watcher, while
+     * `codegraph sync` (a fresh process) honoured it immediately: the CLI
+     * removed a newly excluded file and the watcher re-added it seconds later.
+     * `loadExtensionOverrides()` on the same filter line was already read live
+     * (mtime-cached), so two fields of the same config file disagreed.
+     *
+     * Rebuilding costs one `git ls-files` pass (embedded-repo discovery), which
+     * is fine per config edit — never per event. Replacing the field is enough
+     * for both strategies: the recursive handler and the per-directory
+     * `shouldIgnoreDir` walk read `this.ignoreMatcher` on every call. The full
+     * scan is required because a scope change has no per-file events: newly
+     * excluded files must be REMOVED from the index and newly included ones
+     * added, and only the scan-diff (which builds its own fresh matcher) knows
+     * which those are.
+     */
+    private refreshScope;
     /**
      * A deleted DIRECTORY arrives as one event on the directory's own path —
      * no source extension, so the source-file filter drops it, and the files

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

@@ -1 +1 @@
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package/dist/sync/watcher.js

@@ -282,11 +282,13 @@ class FileWatcher {
      * deterministically gate on watcher readiness.
      */
     readyWaiters = [];
-    // The shared scope matcher (built-in defaults + project .gitignore, with
-    // embedded child repos matched by their OWN rules — #514), built once at
-    // start(). Same source of truth the indexer uses, so watcher scope can
-    // never diverge from index scope. An embedded repo created after start()
-    // joins the scope on the next watcher restart / re-index.
+    // The shared scope matcher (built-in defaults + project .gitignore + the
+    // `codegraph.json` exclude/include rules, with embedded child repos matched
+    // by their OWN rules — #514), built at start() and REBUILT whenever one of
+    // the files it is derived from changes (see `refreshScope`, #1590). Same
+    // source of truth the indexer uses, so watcher scope can never diverge from
+    // index scope. An embedded repo created after start() joins the scope on
+    // the next scope refresh / watcher restart / re-index.
     ignoreMatcher = null;
     projectRoot;
     debounceMs;
@@ -520,8 +522,25 @@ class FileWatcher {
             return;
         if (this.isAlwaysIgnored(rel))
             return;
+        // The two root files the scope matcher is derived from are handled BEFORE
+        // the matcher is consulted: a user `exclude` pattern that happens to cover
+        // them (`*.json`, `.*`) must not be able to hide their own edits (#1590).
+        if (rel === project_config_1.PROJECT_CONFIG_FILENAME || rel === '.gitignore') {
+            this.refreshScope(rel);
+            return;
+        }
         if (this.ignoreMatcher && this.ignoreMatcher.ignores(rel))
             return;
+        // A nested `.gitignore` (an embedded child repo's own rules, #514, or a
+        // subdirectory rule the git-backed full scan honors) is only a scope
+        // change when it sits INSIDE the current scope — checked after the matcher
+        // on purpose, so the thousands of package-local `.gitignore`s an
+        // `npm install` writes under an ignored `node_modules/` never trigger a
+        // rebuild storm.
+        if (rel.endsWith('/.gitignore')) {
+            this.refreshScope(rel);
+            return;
+        }
         if (!(0, extraction_1.isSourceFile)(rel, (0, project_config_1.loadExtensionOverrides)(this.projectRoot))) {
             this.maybeScheduleForRemovedDir(rel);
             return;
@@ -537,6 +556,33 @@ class FileWatcher {
         }
         this.scheduleSync();
     }
+    /**
+     * A scope-defining file changed (`codegraph.json`, a `.gitignore`): rebuild
+     * the ignore matcher and make the next sync a FULL reconcile (#1590).
+     *
+     * The matcher used to be built once in `start()` and kept for the watcher's
+     * lifetime — in a long-lived MCP daemon that meant a `codegraph.json`
+     * created or edited after startup was invisible to the live watcher, while
+     * `codegraph sync` (a fresh process) honoured it immediately: the CLI
+     * removed a newly excluded file and the watcher re-added it seconds later.
+     * `loadExtensionOverrides()` on the same filter line was already read live
+     * (mtime-cached), so two fields of the same config file disagreed.
+     *
+     * Rebuilding costs one `git ls-files` pass (embedded-repo discovery), which
+     * is fine per config edit — never per event. Replacing the field is enough
+     * for both strategies: the recursive handler and the per-directory
+     * `shouldIgnoreDir` walk read `this.ignoreMatcher` on every call. The full
+     * scan is required because a scope change has no per-file events: newly
+     * excluded files must be REMOVED from the index and newly included ones
+     * added, and only the scan-diff (which builds its own fresh matcher) knows
+     * which those are.
+     */
+    refreshScope(rel) {
+        (0, errors_1.logDebug)('Scope config changed; rebuilding watcher scope', { file: rel });
+        this.ignoreMatcher = (0, extraction_1.buildScopeIgnore)(this.projectRoot);
+        this.needsFullScan = true;
+        this.scheduleSync();
+    }
     /**
      * A deleted DIRECTORY arrives as one event on the directory's own path —
      * no source extension, so the source-file filter drops it, and the files