gitnexus 1.6.11-rc.47 → 1.6.11-rc.48

package/README.md

@@ -236,7 +236,8 @@ gitnexus uninstall               # Preview removal of GitNexus MCP/skills/hooks
 gitnexus analyze [path]          # Index a repository (or update stale index)
 gitnexus analyze [path] --watch  # Watch local files and serialize incremental refreshes
 gitnexus analyze --repair-fts    # Fast path: rebuild/verify only FTS indexes on existing index data
-gitnexus analyze --force         # Full rebuild: re-parse + graph rebuild + FTS rebuild
+gitnexus analyze --force         # Rebuild graph + FTS; may reuse unchanged parser output
+gitnexus analyze --no-parse-cache # Re-parse every source file, then rebuild graph + FTS
 gitnexus analyze --embeddings    # Enable embedding generation (slower, better search)
 gitnexus embeddings install      # Fetch the optional local embedding stack on demand (--cuda, --force)
 gitnexus analyze --skills        # Generate repo-specific skill files from detected communities

package/dist/_shared/integrations/circuit-breaker.d.ts.map

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package/dist/_shared/integrations/circuit-breaker.js.map

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package/dist/_shared/integrations/resilient-fetch.d.ts.map

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package/dist/_shared/language-detection.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"language-detection.d.ts","sourceRoot":"","sources":["../src/language-detection.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,kBAAkB,EAAE,MAAM,gBAAgB,CAAC;AA0DpD;;;;GAIG;AACH,eAAO,MAAM,uBAAuB,GAAI,UAAU,MAAM,KAAG,OACQ,CAAC;AAEpE;;;GAGG;AACH,eAAO,MAAM,uBAAuB,GAAI,UAAU,MAAM,KAAG,kBAAkB,GAAG,IAkB/E,CAAC;AAyDF;;;;GAIG;AACH,eAAO,MAAM,6BAA6B,GAAI,UAAU,MAAM,KAAG,MAUhE,CAAC"}

package/dist/_shared/lbug/schema-constants.d.ts

@@ -7,10 +7,10 @@
  * Full DDL schemas remain in each package's own schema.ts because
  * the CLI uses native LadybugDB and the web uses WASM.
  */
-export declare const NODE_TABLES: readonly ['File', 'Folder', 'Function', 'Class', 'Interface', 'Method', 'CodeElement', 'Community', 'Process', 'Section', 'Struct', 'Enum', 'Macro', 'Typedef', 'Union', 'Namespace', 'Trait', 'Impl', 'TypeAlias', 'Const', 'Static', 'Variable', 'Property', 'Record', 'Delegate', 'Annotation', 'Constructor', 'Template', 'Module', 'Route', 'Tool', 'Destination', 'BasicBlock'];
+export declare const NODE_TABLES: readonly ["File", "Folder", "Function", "Class", "Interface", "Method", "CodeElement", "Community", "Process", "Section", "Struct", "Enum", "Macro", "Typedef", "Union", "Namespace", "Trait", "Impl", "TypeAlias", "Const", "Static", "Variable", "Property", "Record", "Delegate", "Annotation", "Constructor", "Template", "Module", "Route", "Tool", "Destination", "BasicBlock"];
 export type NodeTableName = (typeof NODE_TABLES)[number];
 export declare const REL_TABLE_NAME = "CodeRelation";
-export declare const REL_TYPES: readonly ['CONTAINS', 'DEFINES', 'IMPORTS', 'CALLS', 'EXTENDS', 'IMPLEMENTS', 'HAS_METHOD', 'HAS_PROPERTY', 'ACCESSES', 'METHOD_OVERRIDES', 'OVERRIDES', 'METHOD_IMPLEMENTS', 'MEMBER_OF', 'STEP_IN_PROCESS', 'HANDLES_ROUTE', 'PUBLISHES_TO', 'CONSUMES_FROM', 'FETCHES', 'HANDLES_TOOL', 'ENTRY_POINT_OF', 'WRAPS', 'QUERIES', 'INJECTS', 'CONDITIONAL_ON', 'DECLARES', 'ADVISED_BY', 'CFG', 'REACHING_DEF', 'TAINTED', 'SANITIZES', 'TAINT_PATH', 'CDG', 'POST_DOMINATE'];
+export declare const REL_TYPES: readonly ["CONTAINS", "DEFINES", "IMPORTS", "CALLS", "EXTENDS", "IMPLEMENTS", "HAS_METHOD", "HAS_PROPERTY", "ACCESSES", "METHOD_OVERRIDES", "OVERRIDES", "METHOD_IMPLEMENTS", "MEMBER_OF", "STEP_IN_PROCESS", "HANDLES_ROUTE", "PUBLISHES_TO", "CONSUMES_FROM", "FETCHES", "HANDLES_TOOL", "ENTRY_POINT_OF", "WRAPS", "QUERIES", "INJECTS", "CONDITIONAL_ON", "DECLARES", "ADVISED_BY", "CFG", "REACHING_DEF", "TAINTED", "SANITIZES", "TAINT_PATH", "CDG", "POST_DOMINATE"];
 export type RelType = (typeof REL_TYPES)[number];
 export declare const EMBEDDING_TABLE_NAME = "CodeEmbedding";
 //# sourceMappingURL=schema-constants.d.ts.map

package/dist/_shared/lbug/schema-constants.d.ts.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/evidence-weights.d.ts.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/registries/field-registry.js.map

@@ -1 +1 @@
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+{"version":3,"file":"field-registry.js","sourceRoot":"","sources":["../../../src/scope-resolution/registries/field-registry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAGH,OAAO,EAAE,UAAU,EAAyB,MAAM,kBAAkB,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,MAAM,cAAc,CAAC;AAW3C,MAAM,UAAU,kBAAkB,CAAC,GAAoB;IACrD,OAAO;QACL,MAAM,CAAC,IAAY,EAAE,KAAc,EAAE,UAA8B,EAAE;YACnE,MAAM,MAAM,GAAqB;gBAC/B,aAAa,EAAE,WAAW;gBAC1B,sBAAsB,EAAE,IAAI;gBAC5B,sBAAsB,EAAE,OAAO,CAAC,sBAAsB,IAAI,IAAI;gBAC9D,GAAG,CAAC,OAAO,CAAC,gBAAgB,KAAK,SAAS;oBACxC,CAAC,CAAC,EAAE,gBAAgB,EAAE,OAAO,CAAC,gBAAgB,EAAE;oBAChD,CAAC,CAAC,EAAE,CAAC;aACR,CAAC;YACF,OAAO,UAAU,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,CAAC,CAAC;QAC9C,CAAC;KACF,CAAC;AACJ,CAAC"}

package/dist/_shared/scope-resolution/registries/method-registry.js.map

@@ -1 +1 @@
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+{"version":3,"file":"method-registry.js","sourceRoot":"","sources":["../../../src/scope-resolution/registries/method-registry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAGH,OAAO,EAAE,UAAU,EAAyB,MAAM,kBAAkB,CAAC;AAErE,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAqB5C,MAAM,UAAU,mBAAmB,CAAC,GAAoB;IACtD,OAAO;QACL,MAAM,CAAC,IAAY,EAAE,KAAc,EAAE,UAA+B,EAAE;YACpE,MAAM,MAAM,GAAqB;gBAC/B,aAAa,EAAE,YAAY;gBAC3B,sBAAsB,EAAE,IAAI;gBAC5B,sBAAsB,EAAE,OAAO,CAAC,sBAAsB,IAAI,IAAI;gBAC9D,GAAG,CAAC,OAAO,CAAC,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,OAAO,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBACzE,GAAG,CAAC,OAAO,CAAC,gBAAgB,KAAK,SAAS;oBACxC,CAAC,CAAC,EAAE,gBAAgB,EAAE,OAAO,CAAC,gBAAgB,EAAE;oBAChD,CAAC,CAAC,EAAE,CAAC;aACR,CAAC;YACF,OAAO,UAAU,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,CAAC,CAAC;QAC9C,CAAC;KACF,CAAC;AACJ,CAAC"}

package/dist/_shared/scope-resolution/scope-tree.d.ts.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/scope-tree.js.map

@@ -1 +1 @@
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package/dist/cli/analyze-options.d.ts

@@ -20,6 +20,8 @@ export interface AnalyzeOptions {
     /** Watch quiet period in milliseconds. */
     debounce?: string;
     force?: boolean;
+    /** Commander negated flag: false only when --no-parse-cache is passed. */
+    parseCache?: boolean;
     repairFts?: boolean;
     /**
      * Embedding generation toggle. Commander parses `--embeddings [limit]` as:

package/dist/cli/analyze-watch.js

@@ -64,6 +64,7 @@ export async function resolveWatchOptions(repoPath, cli, baseline, reportIgnored
     const merged = mergeAnalyzeOptions(cli, config);
     const unsupported = [
         ['--force', cli.force],
+        ['--no-parse-cache', cli.parseCache === false],
         ['--repair-fts', cli.repairFts],
         ['--embeddings', cli.embeddings],
         ['--drop-embeddings', cli.dropEmbeddings],

package/dist/cli/analyze.js

@@ -940,9 +940,9 @@ const analyzeCommandImpl = async (inputPath, cliOptions, runnerIdentityAtBootstr
             }
         }
     }
-    if (options.repairFts && options.force) {
-        cliError('  Cannot combine `--repair-fts` with `--force`. ' +
-            'Use `--repair-fts` for fast FTS-only repair, or `--force` for a full rebuild.\n');
+    if (options.repairFts && (options.force || options.parseCache === false)) {
+        cliError('  Cannot combine `--repair-fts` with a full rebuild. ' +
+            'Use `--repair-fts` alone for fast FTS-only repair.\n');
         process.exitCode = 1;
         return;
     }
@@ -1084,10 +1084,11 @@ const analyzeCommandImpl = async (inputPath, cliOptions, runnerIdentityAtBootstr
         const skipAgentsMd = skipAll || options.skipAgentsMd;
         const skipSkills = skipAll || options.skipSkills;
         const runOptions = {
-            // Pipeline re-index — OR'd with --skills because skill generation
-            // needs a fresh pipelineResult. Has no bearing on the registry
-            // collision guard (see allowDuplicateName below).
-            force: options.force || options.skills,
+            // Pipeline re-index — OR'd with --skills because skill generation needs
+            // a fresh pipelineResult, and with --no-parse-cache because bypassing
+            // parser output is meaningful only when the pipeline runs.
+            force: options.force || options.skills || options.parseCache === false,
+            useParseCache: options.parseCache !== false,
             repairFts: options.repairFts,
             embeddings: embeddingsEnabled,
             embeddingsNodeLimit,

package/dist/cli/help-i18n.js

@@ -49,6 +49,7 @@ const OPTION_DESCRIPTION_KEYS = {
     '|-V, --version': 'help.option.version',
     'setup|-c, --coding-agent <agents>': 'help.option.setup.codingAgent',
     'analyze|-f, --force': 'help.option.analyze.force',
+    'analyze|--no-parse-cache': 'help.option.analyze.noParseCache',
     'analyze|--repair-fts': 'help.option.analyze.repairFts',
     'analyze|--embeddings [limit]': 'help.option.analyze.embeddings',
     'analyze|--drop-embeddings': 'help.option.analyze.dropEmbeddings',

package/dist/cli/i18n/en.d.ts

@@ -163,7 +163,8 @@ export declare const en: {
     readonly 'help.command.group.query.description': "Search execution flows across all repos in a group";
     readonly 'help.command.group.contracts.description': "Inspect Contract Registry";
     readonly 'help.option.setup.codingAgent': "Configure only these coding agents (comma-separated or repeatable)";
-    readonly 'help.option.analyze.force': "Force full re-index even if up to date";
+    readonly 'help.option.analyze.force': "Force graph and FTS rebuild; unchanged parser output may be reused";
+    readonly 'help.option.analyze.noParseCache': "Re-parse every source file instead of replaying cached parser output";
     readonly 'help.option.analyze.repairFts': "Repair/rebuild search FTS indexes without full re-analysis";
     readonly 'help.option.analyze.embeddings': "Enable embedding generation for semantic search (off by default). Optional [limit] overrides the 50,000-node safety cap; pass 0 to disable the cap entirely.";
     readonly 'help.option.analyze.dropEmbeddings': "Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` preserves any embeddings already present in the index.";

package/dist/cli/i18n/en.js

@@ -165,7 +165,8 @@ export const en = {
     'help.command.group.query.description': 'Search execution flows across all repos in a group',
     'help.command.group.contracts.description': 'Inspect Contract Registry',
     'help.option.setup.codingAgent': 'Configure only these coding agents (comma-separated or repeatable)',
-    'help.option.analyze.force': 'Force full re-index even if up to date',
+    'help.option.analyze.force': 'Force graph and FTS rebuild; unchanged parser output may be reused',
+    'help.option.analyze.noParseCache': 'Re-parse every source file instead of replaying cached parser output',
     'help.option.analyze.repairFts': 'Repair/rebuild search FTS indexes without full re-analysis',
     'help.option.analyze.embeddings': 'Enable embedding generation for semantic search (off by default). Optional [limit] overrides the 50,000-node safety cap; pass 0 to disable the cap entirely.',
     'help.option.analyze.dropEmbeddings': 'Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` preserves any embeddings already present in the index.',

package/dist/cli/i18n/resources.d.ts

@@ -164,7 +164,8 @@ export declare const cliResources: {
         readonly 'help.command.group.query.description': "Search execution flows across all repos in a group";
         readonly 'help.command.group.contracts.description': "Inspect Contract Registry";
         readonly 'help.option.setup.codingAgent': "Configure only these coding agents (comma-separated or repeatable)";
-        readonly 'help.option.analyze.force': "Force full re-index even if up to date";
+        readonly 'help.option.analyze.force': "Force graph and FTS rebuild; unchanged parser output may be reused";
+        readonly 'help.option.analyze.noParseCache': "Re-parse every source file instead of replaying cached parser output";
         readonly 'help.option.analyze.repairFts': "Repair/rebuild search FTS indexes without full re-analysis";
         readonly 'help.option.analyze.embeddings': "Enable embedding generation for semantic search (off by default). Optional [limit] overrides the 50,000-node safety cap; pass 0 to disable the cap entirely.";
         readonly 'help.option.analyze.dropEmbeddings': "Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` preserves any embeddings already present in the index.";
@@ -435,6 +436,7 @@ export declare const cliResources: {
         'help.command.group.contracts.description': string;
         'help.option.setup.codingAgent': string;
         'help.option.analyze.force': string;
+        'help.option.analyze.noParseCache': string;
         'help.option.analyze.repairFts': string;
         'help.option.analyze.embeddings': string;
         'help.option.analyze.dropEmbeddings': string;

package/dist/cli/i18n/zh-CN.d.ts

@@ -164,6 +164,7 @@ export declare const zhCN: {
     'help.command.group.contracts.description': string;
     'help.option.setup.codingAgent': string;
     'help.option.analyze.force': string;
+    'help.option.analyze.noParseCache': string;
     'help.option.analyze.repairFts': string;
     'help.option.analyze.embeddings': string;
     'help.option.analyze.dropEmbeddings': string;

package/dist/cli/i18n/zh-CN.js

@@ -163,7 +163,8 @@ export const zhCN = {
     'help.command.group.query.description': '跨仓库组所有仓库搜索执行流程',
     'help.command.group.contracts.description': '查看 Contract Registry',
     'help.option.setup.codingAgent': '仅配置这些编码代理（逗号分隔或重复传入）',
-    'help.option.analyze.force': '即使已是最新也强制完整重建索引',
+    'help.option.analyze.force': '强制重建图和 FTS；未更改的解析器输出可能被复用',
+    'help.option.analyze.noParseCache': '重新解析每个源文件，不重放缓存的解析器输出',
     'help.option.analyze.repairFts': '修复/重建搜索 FTS 索引，不执行完整重新分析',
     'help.option.analyze.embeddings': '启用语义搜索的嵌入生成（默认关闭）。可选 [limit] 覆盖 50,000 节点安全上限；传 0 可完全禁用上限。',
     'help.option.analyze.dropEmbeddings': '重建时删除现有嵌入。默认情况下，未传 `--embeddings` 的 `analyze` 会保留索引中已有嵌入。',

package/dist/cli/index.js

@@ -48,7 +48,8 @@ program
     .description('Index a repository (full analysis)')
     .option('--watch', 'Keep the index current with serialized incremental refreshes')
     .option('--debounce <ms>', 'Watch quiet period before refreshing (default: 300 milliseconds)')
-    .option('-f, --force', 'Force full re-index even if up to date')
+    .option('-f, --force', 'Force graph and FTS rebuild; unchanged parser output may be reused')
+    .option('--no-parse-cache', 'Re-parse every source file instead of replaying cached parser output')
     .option('--repair-fts', 'Repair/rebuild search FTS indexes without full re-analysis')
     .option('--embeddings [limit]', 'Enable embedding generation for semantic search (off by default). ' +
     'Optional [limit] overrides the 50,000-node safety cap; pass 0 to disable the cap entirely.')

package/dist/core/ingestion/pipeline-phases/parse-impl.d.ts

@@ -97,6 +97,8 @@ export declare function runChunkedParseAndResolve(graph: KnowledgeGraph, scanned
     usedWorkerPool: boolean;
     /** Files dispatched to parser workers after parse-cache lookup. */
     reparsedFileCount: number;
+    /** Files restored from parse-cache chunks without parser-worker dispatch. */
+    parseCacheHitFileCount: number;
     /** Worker-produced ParsedFile artifacts aggregated across chunks.
      *  Threaded into scope-resolution as a re-extract cache so the warm-
      *  cache analyze run can skip the dominant `extractParsedFile` cost

package/dist/core/ingestion/pipeline-phases/parse-impl.js

@@ -557,6 +557,7 @@ export async function runChunkedParseAndResolve(graph, scannedFiles, allPaths, t
         : new Map();
     let chunkCacheHits = 0;
     let chunkCacheMisses = 0;
+    let parseCacheHitFileCount = 0;
     let reparsedFileCount = 0;
     try {
         // U1 — bounded chunk concurrency (B1 from PR #1693 review): pre-fetch
@@ -816,6 +817,7 @@ export async function runChunkedParseAndResolve(graph, scannedFiles, allPaths, t
                     pendingWorkerChunk = null;
                 }
                 chunkCacheHits++;
+                parseCacheHitFileCount += chunkFiles.length;
                 const chunkWorkerData = mergeChunkResults(graph, symbolTable, cachedRaw, exportedTypeMap);
                 if (isDev) {
                     logger.info(`📦 parse-cache HIT: chunk ${chunkIdx + 1}/${numChunks} (${chunkFiles.length} files, ${chunkHash?.slice(0, 8) ?? 'unknown'})`);
@@ -1324,6 +1326,7 @@ export async function runChunkedParseAndResolve(graph, scannedFiles, allPaths, t
         // is intentionally measured at dispatch time rather than inferred from
         // the git/hash diff.
         reparsedFileCount,
+        parseCacheHitFileCount,
         // Per-file ParsedFile artifacts produced by workers' calls to
         // `extractParsedFile`. Consumed by scope-resolution as a re-extraction
         // cache: when the file's ParsedFile is here, scope-resolution skips its own

package/dist/core/ingestion/pipeline.js

@@ -120,7 +120,7 @@ export const runPipelineFromRepo = async (repoPath, onProgress, options) => {
         graphEmitSink?.close();
     }
     // Extract final results for the PipelineResult contract
-    const { totalFiles, usedWorkerPool, reparsedFileCount, unavailableScopeLanguageFiles } = getPhaseOutput(results, 'parse');
+    const { totalFiles, usedWorkerPool, reparsedFileCount, parseCacheHitFileCount, unavailableScopeLanguageFiles, } = getPhaseOutput(results, 'parse');
     let communityResult;
     let processResult;
     const scopeResolutionOutput = getPhaseOutput(results, 'scopeResolution');
@@ -168,6 +168,7 @@ export const runPipelineFromRepo = async (repoPath, onProgress, options) => {
         undecidedSatisfaction,
         usedWorkerPool,
         reparsedFileCount,
+        parseCacheHitFileCount,
         scopeExtractionFailures,
         unavailableScopeLanguageFiles,
         pdgEmitManifest,

package/dist/core/run-analyze.d.ts

@@ -17,12 +17,19 @@ export interface AnalyzeCallbacks {
 }
 export interface AnalyzeOptions {
     /**
-     * Force a full re-index of the pipeline. Callers may OR this with
-     * other flags that imply re-analysis (e.g. `--skills`), so the value
-     * here is the PIPELINE-force signal, NOT the registry-collision
-     * bypass. See `allowDuplicateName` below.
+     * Rebuild the graph and FTS. Parser output is still reused from the
+     * content-addressed parse cache unless `useParseCache` is false.
+     * Callers may OR this with other flags that imply re-analysis
+     * (e.g. `--skills`), so the value here is the PIPELINE-force signal,
+     * NOT the registry-collision bypass. See `allowDuplicateName` below.
      */
     force?: boolean;
+    /**
+     * Reuse content-addressed parser output. Defaults to true. When false,
+     * analysis reparses every file and publishes a new parse-cache generation
+     * only after a successful run (live shards stay untouched if the run fails).
+     */
+    useParseCache?: boolean;
     /** Repair only search indexes without re-running full parsing/indexing. */
     repairFts?: boolean;
     /** Emit per-index FTS create logs. */

package/dist/core/run-analyze.js

@@ -46,8 +46,8 @@ import { shadowCandidatesFor } from './incremental/shadow-candidates.js';
 import { shouldEscalateIncrementalWrite } from './incremental/escalation-gate.js';
 import { ftsTablesAmong, incrementalFtsTablesFromGraph, nodeTablesForIncrementalDelete, shouldPreservePersistedDerivedGraph, } from './incremental/derived-writeback.js';
 import { NODE_TABLES } from './lbug/schema.js';
-import { loadParseCache, saveParseCache, pruneCache, PARSE_CACHE_VERSION, } from '../storage/parse-cache.js';
-import { getDurableParsedFileDir, pruneAndSaveDurableParsedFileStore, } from '../storage/parsedfile-store.js';
+import { loadParseCache, saveParseCache, pruneCache, PARSE_CACHE_VERSION, createColdParseRebuildDir, emptyParseCache, forgetCreatedParseCacheDir, } from '../storage/parse-cache.js';
+import { mergeStagedDurableParsedFileStore } from '../storage/parsedfile-store.js';
 import { getCurrentCommit, getCurrentBranch, getRemoteUrl, hasGitDir, getInferredRepoName, isWorkingTreeDirty, listWorkingTreeDirtyPaths, resolveRepoIdentityRoot, } from '../storage/git.js';
 import { isGitNexusManagedPath } from '../storage/gitnexus-managed-paths.js';
 import { getMaxFileSizeBytes } from './ingestion/utils/max-file-size.js';
@@ -553,6 +553,17 @@ async function resolveWriteTarget(repoPath, options) {
         metaDir: path.dirname(metaPath),
     };
 }
+async function removeColdParseRebuildDir(dir, ignoreErrors) {
+    if (!dir)
+        return;
+    try {
+        await fs.rm(dir, { recursive: true, force: true });
+    }
+    catch (err) {
+        if (!ignoreErrors)
+            throw err;
+    }
+}
 /**
  * Run the full analysis under an exclusive, index-directory-scoped write lock
  * (#2658). A second concurrent `analyze` on the same slot waits here for the
@@ -630,6 +641,7 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
     // selects a `branches/<slug>/` sub-slot only for an explicit `--branch` that
     // does not own the flat slot. See resolveWriteTarget for the full contract.
     const { storagePath, repoHasGit, currentCommit, branchLabel, placement, lbugPath, metaDir } = writeTarget;
+    let coldParseRebuildDir;
     // Start each analyze with a clean buffer-pool hint: any pre-pipeline DB open
     // (e.g. the embeddings-cache open) falls back to the default until the hint is
     // set from the built graph below, so a prior run's size can't leak in.
@@ -1165,6 +1177,12 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
         log('AsyncAPI document reading disabled; rebuilding to remove document-derived evidence.');
         options = { ...options, force: true };
     }
+    // Programmatic `useParseCache: false` must set force or the up-to-date
+    // guard returns before the empty-cache construction below.
+    if (options.useParseCache === false && !options.force) {
+        log('Parser cache bypass requested; forcing a full rebuild so unchanged files are re-parsed.');
+        options = { ...options, force: true };
+    }
     // ── Early-return: already up to date ──────────────────────────────
     if (existingMeta &&
         !existingMeta.embeddingCheckpoint &&
@@ -1362,11 +1380,17 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
         }
     }
     // ── Load incremental parse cache ──────────────────────────────────
-    // Content-addressed: safe to reuse across `--force` runs (chunks whose
-    // file contents haven't changed produce identical worker output).
-    // Loaded into a single ParseCache object that the pipeline mutates
-    // in-place (cache hits leave entries unchanged; misses add new ones).
-    const parseCache = await loadParseCache(storagePath);
+    // Content-addressed: `--force` reuses parser shards; `useParseCache: false`
+    // stages a new generation under a run-unique parse-rebuild.* dir and publishes
+    // after success. Unique because index locks are per branch slot while this
+    // cache root is shared across branches.
+    if (options.useParseCache === false) {
+        coldParseRebuildDir = await createColdParseRebuildDir(storagePath);
+        forgetCreatedParseCacheDir(coldParseRebuildDir);
+    }
+    const parseCache = options.useParseCache === false
+        ? emptyParseCache(coldParseRebuildDir)
+        : await loadParseCache(storagePath);
     // Streamed structural emit (#2680). Resolved ONCE, so the pipeline flag and
     // the CSV-dir resolution below cannot disagree — and resolved HERE, not at
     // function entry, because the POSITION is load-bearing: the gate is
@@ -1400,49 +1424,63 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
         repoHasGit &&
         !schemaFingerprintMismatch(existingMeta.schemaFingerprint);
     // ── Phase 1: Full Pipeline (0–60%) ────────────────────────────────
-    const pipelineResult = await runPipelineFromRepo(repoPath, (p) => {
-        const phaseLabel = PHASE_LABELS[p.phase] || p.phase;
-        const scaled = Math.round(p.percent * 0.6);
-        const message = p.detail
-            ? `${p.message || phaseLabel} (${p.detail})`
-            : p.message || phaseLabel;
-        progress(p.phase, scaled, message);
-    }, {
-        parseCache,
-        workerPoolSize: options.workerPoolSize,
-        // CFG/PDG opt-in (#2081 M1). PipelineOptions.pdg fans out to the worker
-        // build gate (workerData.pdg) and the scope-resolution emit gate.
-        pdg: options.pdg === true,
-        pdgMaxFunctionLines: options.pdgMaxFunctionLines,
-        pdgMaxEdgesPerFunction: options.pdgMaxEdgesPerFunction,
-        pdgMaxReachingDefEdgesPerFunction: options.pdgMaxReachingDefEdgesPerFunction,
-        pdgMaxCdgEdgesPerFunction: options.pdgMaxCdgEdgesPerFunction,
-        pdgMaxTaintFindingsPerFunction: options.pdgMaxTaintFindingsPerFunction,
-        pdgMaxTaintHops: options.pdgMaxTaintHops,
-        pdgMaxInterprocFindings: options.pdgMaxInterprocFindings,
-        pdgMaxInterprocHops: options.pdgMaxInterprocHops,
-        pdgMaxInterprocEdges: options.pdgMaxInterprocEdges,
-        // Streaming/chunked PDG emit (#2202) — gated to full-rebuild runs
-        // (force === true) so the incremental writeback never reads back an
-        // offloaded BasicBlock layer. Memory-only; byte-identical output.
-        streamPdgEmit: resolveStreamPdgEmit(options),
-        pdgEmitChunkSize: resolvePdgEmitChunkSize(options),
-        // Streamed structural emit (#2680) — same full-rebuild gate as the PDG
-        // toggle above, for the same incremental-writeback reason.
-        streamGraphEmit: streamGraphEmitActive,
-        // Resolved ONLY when streaming is active: on a Windows non-ASCII storage
-        // path this helper mkdtempSyncs a real directory, so evaluating it
-        // unconditionally would leak one temp dir per analyze even with the flag
-        // off. The PDG sibling resolves inside its guard for the same reason.
-        graphEmitCsvDir: streamGraphEmitActive
-            ? resolveNativeSafeStorageDir(storagePath, 'graph-csv')
-            : undefined,
-        fetchWrappers: options.fetchWrappers,
-        skipDerivedGraphPhases,
-        springActuatorPath: options.springActuatorPath,
-        asyncApiSpecPath: options.asyncApiSpecPath,
-        springActuatorScanExclusions,
-    });
+    let pipelineResult;
+    try {
+        pipelineResult = await runPipelineFromRepo(repoPath, (p) => {
+            const phaseLabel = PHASE_LABELS[p.phase] || p.phase;
+            const scaled = Math.round(p.percent * 0.6);
+            const message = p.detail
+                ? `${p.message || phaseLabel} (${p.detail})`
+                : p.message || phaseLabel;
+            progress(p.phase, scaled, message);
+        }, {
+            parseCache,
+            workerPoolSize: options.workerPoolSize,
+            // CFG/PDG opt-in (#2081 M1). PipelineOptions.pdg fans out to the worker
+            // build gate (workerData.pdg) and the scope-resolution emit gate.
+            pdg: options.pdg === true,
+            pdgMaxFunctionLines: options.pdgMaxFunctionLines,
+            pdgMaxEdgesPerFunction: options.pdgMaxEdgesPerFunction,
+            pdgMaxReachingDefEdgesPerFunction: options.pdgMaxReachingDefEdgesPerFunction,
+            pdgMaxCdgEdgesPerFunction: options.pdgMaxCdgEdgesPerFunction,
+            pdgMaxTaintFindingsPerFunction: options.pdgMaxTaintFindingsPerFunction,
+            pdgMaxTaintHops: options.pdgMaxTaintHops,
+            pdgMaxInterprocFindings: options.pdgMaxInterprocFindings,
+            pdgMaxInterprocHops: options.pdgMaxInterprocHops,
+            pdgMaxInterprocEdges: options.pdgMaxInterprocEdges,
+            // Streaming/chunked PDG emit (#2202) — gated to full-rebuild runs
+            // (force === true) so the incremental writeback never reads back an
+            // offloaded BasicBlock layer. Memory-only; byte-identical output.
+            streamPdgEmit: resolveStreamPdgEmit(options),
+            pdgEmitChunkSize: resolvePdgEmitChunkSize(options),
+            // Streamed structural emit (#2680) — same full-rebuild gate as the PDG
+            // toggle above, for the same incremental-writeback reason.
+            streamGraphEmit: streamGraphEmitActive,
+            // Resolved ONLY when streaming is active: on a Windows non-ASCII storage
+            // path this helper mkdtempSyncs a real directory, so evaluating it
+            // unconditionally would leak one temp dir per analyze even with the flag
+            // off. The PDG sibling resolves inside its guard for the same reason.
+            graphEmitCsvDir: streamGraphEmitActive
+                ? resolveNativeSafeStorageDir(storagePath, 'graph-csv')
+                : undefined,
+            fetchWrappers: options.fetchWrappers,
+            skipDerivedGraphPhases,
+            springActuatorPath: options.springActuatorPath,
+            asyncApiSpecPath: options.asyncApiSpecPath,
+            springActuatorScanExclusions,
+        });
+    }
+    catch (err) {
+        await removeColdParseRebuildDir(coldParseRebuildDir, true);
+        throw err;
+    }
+    if (options.force && (pipelineResult.parseCacheHitFileCount ?? 0) > 0) {
+        log(`Rebuilt the graph and FTS while reusing cached parser output for ` +
+            `${pipelineResult.parseCacheHitFileCount} file(s) ` +
+            `(parse cache ${PARSE_CACHE_VERSION}). ` +
+            `For same-version capture/query development changes, increment SCHEMA_BUMP in ` +
+            `src/storage/parse-cache.ts to invalidate parser output.`);
+    }
     // ── Phase 2: LadybugDB (60–85%) ──────────────────────────────────
     progress('lbug', 60, 'Loading into LadybugDB...');
     // Compute current per-file content hashes from the pipeline's File nodes.
@@ -3180,50 +3218,8 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
         // meta.indexedAt = T_new while lbugPath still resolves to the pre-swap
         // inode (which latched the reader on the stale index permanently). The meta
         // object is fully computed at this point; only its write is deferred.
-        // Persist the incremental parse cache for the next run. Wraps in
-        // try/catch so a cache-write failure never breaks an otherwise
-        // successful indexing run. Prune stale chunk-hash entries first so
-        // the cache file size stays bounded across runs (chunks whose
-        // composition no longer matches anything in the current scan are
-        // dead weight; the parse phase populates `usedKeys` as it processes
-        // chunks).
-        try {
-            // #2106 R6: the parse cache + durable store are shared across branches.
-            // Before pruning to this run's keys, fold in the OTHER branches' recorded
-            // chunk keys so a branch switch doesn't evict their still-live shards.
-            // Adding to usedKeys makes them survive pruneCache AND land in the saved
-            // index (saveParseCache builds the index from usedKeys). Excludes this
-            // run's own meta dir, so a single-branch repo folds in nothing → prune
-            // set byte-identical to today.
-            const { keys: siblingKeys, complete } = await collectBranchCacheKeys(storagePath, metaDir);
-            if (complete) {
-                for (const k of siblingKeys)
-                    parseCache.usedKeys.add(k);
-            }
-            else {
-                // Fail-safe toward retention: a sibling meta was unreadable, so keep
-                // everything currently loaded rather than evict on incomplete info.
-                log('Parse cache: a branch meta was unreadable — retaining all cached chunks (#2106).');
-                for (const k of parseCache.entries.keys())
-                    parseCache.usedKeys.add(k);
-            }
-            const pruned = pruneCache(parseCache, parseCache.usedKeys);
-            if (pruned > 0) {
-                log(`Parse cache: pruned ${pruned} stale chunk entries`);
-            }
-            const savedKeys = await saveParseCache(storagePath, parseCache);
-            // Prune the durable ParsedFile store to EXACTLY the parse cache's
-            // surviving keys (#2038 warm-cache coverage), so the two content-addressed
-            // stores stay coherent: a chunk is "cached" iff both its parse-cache shard
-            // and its durable shards exist. A quarantined chunk (in usedKeys but with
-            // no parse-cache shard) drops its durable subdir here and re-dispatches
-            // next run. Same try/catch — a durable-store write failure must never
-            // break an otherwise successful run (next run treats it as a miss).
-            await pruneAndSaveDurableParsedFileStore(getDurableParsedFileDir(storagePath), PARSE_CACHE_VERSION, new Set(savedKeys));
-        }
-        catch (e) {
-            log(`Warning: could not save parse cache (${e.message}); continuing.`);
-        }
+        // Parse-cache publish waits until after that swap + saveMeta so a failed
+        // registerRepo / close / swap cannot replace live shards (#3153).
         // Forward the --name alias and the registry-collision bypass bit.
         // `allowDuplicateName` is its own concern — independent from the
         // pipeline `force` above. The CLI maps it from
@@ -3244,8 +3240,8 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
         // ── #2354: the flat workspace slot has adopted this run's branch ──────
         // Drop a now-shadowed `branches/<slug>/` sub-index for the same label
         // (unreachable once the flat slot serves it) and align the registry's
-        // top-level branch label. Best-effort like the parse-cache save above
-        // (#2364 review F5): the index is complete and registered, and a failure
+        // top-level branch label. Best-effort (#2364 review F5): the index is
+        // complete and registered, and a failure
         // here leaves only a stale registry label / undeleted shadowed dir —
         // never wrong routing, because the flat meta this run already stamped is
         // what applyBranchScope trusts. Retried by the next content-changing run
@@ -3354,7 +3350,51 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
         // is a crash-safety improvement: a failed swap leaves the previous index
         // live and the next run recovers via the full-rebuild path.
         await saveMeta(metaDir, meta);
+        // Persist the incremental parse cache only after a successful graph
+        // publish (#3153). try/catch so a cache-write failure never breaks an
+        // otherwise successful indexing run. Prune stale chunk-hash entries first
+        // so the cache file size stays bounded across runs (chunks whose
+        // composition no longer matches anything in the current scan are dead
+        // weight; the parse phase populates `usedKeys` as it processes chunks).
+        try {
+            // #2106 R6: the parse cache + durable store are shared across branches.
+            // Before pruning to this run's keys, fold in the OTHER branches' recorded
+            // chunk keys so a branch switch doesn't evict their still-live shards.
+            // Adding to usedKeys makes them survive pruneCache AND land in the saved
+            // index (saveParseCache builds the index from usedKeys). Excludes this
+            // run's own meta dir, so a single-branch repo folds in nothing → prune
+            // set byte-identical to today.
+            const { keys: siblingKeys, complete } = await collectBranchCacheKeys(storagePath, metaDir);
+            if (complete) {
+                for (const k of siblingKeys)
+                    parseCache.usedKeys.add(k);
+            }
+            else {
+                // Fail-safe toward retention: a sibling meta was unreadable, so keep
+                // everything currently loaded rather than evict on incomplete info.
+                log('Parse cache: a branch meta was unreadable — retaining all cached chunks (#2106).');
+                for (const k of parseCache.entries.keys())
+                    parseCache.usedKeys.add(k);
+            }
+            const pruned = pruneCache(parseCache, parseCache.usedKeys);
+            if (pruned > 0) {
+                log(`Parse cache: pruned ${pruned} stale chunk entries`);
+            }
+            const savedKeys = await saveParseCache(storagePath, parseCache);
+            // Prune the durable ParsedFile store to EXACTLY the parse cache's
+            // surviving keys (#2038 warm-cache coverage), so the two content-addressed
+            // stores stay coherent: a chunk is "cached" iff both its parse-cache shard
+            // and its durable shards exist. A quarantined chunk (in usedKeys but with
+            // no parse-cache shard) drops its durable subdir here and re-dispatches
+            // next run. Same try/catch — a durable-store write failure must never
+            // break an otherwise successful run (next run treats it as a miss).
+            await mergeStagedDurableParsedFileStore(storagePath, parseCache.storagePath ?? storagePath, PARSE_CACHE_VERSION, new Set(savedKeys));
+        }
+        catch (e) {
+            log(`Warning: could not save parse cache (${e.message}); continuing.`);
+        }
         progress('done', 100, 'Done');
+        await removeColdParseRebuildDir(coldParseRebuildDir, true);
         return {
             repoName: projectName,
             repoPath,
@@ -3412,6 +3452,7 @@ async function runFullAnalysisInner(repoPath, options, callbacks, writeTarget, r
                 /* swallow — orphan reclamation must never mask the real failure */
             }
         }
+        await removeColdParseRebuildDir(coldParseRebuildDir, true);
         if (liveIndexMutationStarted) {
             // Preserve the original error identity/prototype: callers distinguish
             // IndexLockTimeoutError and other domain failures with `instanceof`.

package/dist/storage/parse-cache.d.ts

@@ -19,9 +19,9 @@
  * - Chunk-level invalidation gives a useful speedup floor (98% on a single
  *   1-of-50 invalidated chunk) without touching the worker.
  *
- * Survives `--force` because it's content-addressed: the same bytes always
- * produce the same key. `--force` only matters for the LadybugDB writeback;
- * the cache itself is always safe to reuse.
+ * `--force` still reuses content-addressed shards (it only rebuilds graph/FTS).
+ * `useParseCache: false` reparses every file, writes a staging generation, and
+ * publishes onto this cache only after a successful analysis.
  */
 import type { ParseWorkerResult } from '../core/ingestion/workers/parse-worker.js';
 export declare const PARSE_CACHE_VERSION: string;
@@ -41,6 +41,21 @@ export type ParseCachePackFile = {
  * independent of scan order and worker count).
  */
 export declare const packParseCacheChunks: (files: readonly ParseCachePackFile[], byteBudget: number) => string[][];
+/**
+ * Per-run staging root for `useParseCache: false`. Parse-cache shards and the
+ * ParsedFile stores write here so a crash cannot mix a new generation into the
+ * live `.gitnexus/parse-cache` / `parsedfile-cache` trees. `saveParseCache`
+ * publishes onto the live `storagePath` only after a successful analysis.
+ */
+export declare const COLD_PARSE_REBUILD_DIRNAME = "parse-rebuild";
+/** Deterministic staging path — tests only. Production uses {@link createColdParseRebuildDir}. */
+export declare const getColdParseRebuildDir: (storagePath: string) => string;
+/**
+ * Unique per analyze process so concurrent `--no-parse-cache` runs on
+ * different branch slots (shared `.gitnexus`, separate index locks) do not
+ * delete each other's staging tree.
+ */
+export declare const createColdParseRebuildDir: (storagePath: string) => Promise<string>;
 /** Runtime view: keyed Map for fast lookup; mutated in place during a run. */
 export interface ParseCache {
     version: string;
@@ -57,6 +72,8 @@ export interface ParseCache {
      * When set, chunk payloads are loaded from / flushed to sharded files on
      * demand instead of retaining every chunk in `entries` for the whole run
      * (#1983 — Linux kernel OOM from duplicate in-memory cache + graph).
+     * May be a per-run staging directory (`getColdParseRebuildDir`) while the
+     * live index root is passed separately to `saveParseCache`.
      */
     storagePath?: string;
     /** Index of chunk hashes known to exist under `storagePath/parse-cache/`. */
@@ -105,6 +122,8 @@ export declare const mapReviver: (_key: string, value: unknown) => unknown;
 export declare const slimParseWorkerResultsForCache: (chunkResults: readonly ParseWorkerResult[]) => ParseWorkerResult[];
 /** Load one chunk shard. Does not retain it in `cache.entries`. */
 export declare const loadParseCacheChunk: (cache: ParseCache, chunkHash: string) => Promise<ParseWorkerResult[] | undefined>;
+/** Drop the mkdir memo after the staging tree is wiped so the next persist recreates it. */
+export declare const forgetCreatedParseCacheDir: (storagePath: string) => void;
 /**
  * Persist one chunk shard and avoid retaining it in RAM for the rest of the
  * run. Falls back to `cache.entries` when `storagePath` is unset (unit tests).
@@ -132,3 +151,4 @@ export declare const saveParseCache: (storagePath: string, cache: ParseCache) =>
  * don't keep their stale entries forever.
  */
 export declare const pruneCache: (cache: ParseCache, usedHashes: ReadonlySet<string>) => number;
+export declare const emptyParseCache: (storagePath?: string) => ParseCache;

package/dist/storage/parse-cache.js

@@ -19,9 +19,9 @@
  * - Chunk-level invalidation gives a useful speedup floor (98% on a single
  *   1-of-50 invalidated chunk) without touching the worker.
  *
- * Survives `--force` because it's content-addressed: the same bytes always
- * produce the same key. `--force` only matters for the LadybugDB writeback;
- * the cache itself is always safe to reuse.
+ * `--force` still reuses content-addressed shards (it only rebuilds graph/FTS).
+ * `useParseCache: false` reparses every file, writes a staging generation, and
+ * publishes onto this cache only after a successful analysis.
  */
 import { createHash } from 'crypto';
 import { createRequire } from 'module';
@@ -804,6 +804,24 @@ export const packParseCacheChunks = (files, byteBudget) => {
 };
 const LEGACY_CACHE_FILENAME = 'parse-cache.json';
 const CACHE_DIRNAME = 'parse-cache';
+/**
+ * Per-run staging root for `useParseCache: false`. Parse-cache shards and the
+ * ParsedFile stores write here so a crash cannot mix a new generation into the
+ * live `.gitnexus/parse-cache` / `parsedfile-cache` trees. `saveParseCache`
+ * publishes onto the live `storagePath` only after a successful analysis.
+ */
+export const COLD_PARSE_REBUILD_DIRNAME = 'parse-rebuild';
+/** Deterministic staging path — tests only. Production uses {@link createColdParseRebuildDir}. */
+export const getColdParseRebuildDir = (storagePath) => path.join(storagePath, COLD_PARSE_REBUILD_DIRNAME);
+/**
+ * Unique per analyze process so concurrent `--no-parse-cache` runs on
+ * different branch slots (shared `.gitnexus`, separate index locks) do not
+ * delete each other's staging tree.
+ */
+export const createColdParseRebuildDir = async (storagePath) => {
+    await fs.mkdir(storagePath, { recursive: true });
+    return fs.mkdtemp(path.join(storagePath, `${COLD_PARSE_REBUILD_DIRNAME}.`));
+};
 const CACHE_INDEX_FILENAME = 'index.json';
 /** Keys on disk always come from `computeChunkHash` — 64-char lowercase hex. */
 const CHUNK_CACHE_KEY_HEX_RE = /^[a-f0-9]{64}$/;
@@ -937,6 +955,10 @@ export const loadParseCacheChunk = async (cache, chunkHash) => {
  * process-scoped, so the Set stays bounded.
  */
 const createdCacheDirs = new Set();
+/** Drop the mkdir memo after the staging tree is wiped so the next persist recreates it. */
+export const forgetCreatedParseCacheDir = (storagePath) => {
+    createdCacheDirs.delete(getCacheDirPath(storagePath));
+};
 /**
  * Persist one chunk shard and avoid retaining it in RAM for the rest of the
  * run. Falls back to `cache.entries` when `storagePath` is unset (unit tests).
@@ -1063,8 +1085,17 @@ export const saveParseCache = async (storagePath, cache) => {
             }
             continue;
         }
-        const existingPath = getCacheChunkPath(storagePath, chunkHash);
-        if (await copyV8CacheIfPresent(existingPath, chunkPath)) {
+        // Cold rebuilds persist mid-run under `cache.storagePath` (staging). Prefer
+        // that generation over a same-hash shard still sitting in the live dir so
+        // we never publish a mixed old/new pair. Sibling-branch keys (#2106) that
+        // this run did not rewrite still copy from the live path.
+        const stagedPath = cache.storagePath !== undefined && cache.storagePath !== storagePath
+            ? getCacheChunkPath(cache.storagePath, chunkHash)
+            : undefined;
+        const livePath = getCacheChunkPath(storagePath, chunkHash);
+        const fromStaged = Boolean(stagedPath && cache.onDiskKeys?.has(chunkHash));
+        const sourcePath = fromStaged && stagedPath ? stagedPath : livePath;
+        if (await copyV8CacheIfPresent(sourcePath, chunkPath)) {
             writtenKeys.push(chunkHash);
         }
     }
@@ -1104,10 +1135,11 @@ export const pruneCache = (cache, usedHashes) => {
     }
     return removed;
 };
-const emptyCache = (storagePath) => ({
+export const emptyParseCache = (storagePath) => ({
     version: PARSE_CACHE_VERSION,
     entries: new Map(),
     usedKeys: new Set(),
     storagePath,
     onDiskKeys: storagePath ? new Set() : undefined,
 });
+const emptyCache = emptyParseCache;

package/dist/storage/parsedfile-store.d.ts

@@ -122,3 +122,10 @@ export declare const loadDurableParsedFileIndex: (durableDir: string, expectedVe
  * for a missing/corrupt shard). The index write is tmp+rename atomic.
  */
 export declare const pruneAndSaveDurableParsedFileStore: (durableDir: string, version: string, keepKeys: ReadonlySet<string>) => Promise<void>;
+/**
+ * Overlay this run's staged durable ParsedFile chunks onto the live store,
+ * then prune the live tree to `keepKeys`. Live chunks this run did not rewrite
+ * (other branches, unused hashes) stay until prune. No-op overlay when the
+ * staged dir is missing.
+ */
+export declare const mergeStagedDurableParsedFileStore: (liveStoragePath: string, stagedStoragePath: string, version: string, keepKeys: ReadonlySet<string>) => Promise<void>;

package/dist/storage/parsedfile-store.js

@@ -605,3 +605,73 @@ export const pruneAndSaveDurableParsedFileStore = async (durableDir, version, ke
     await fs.writeFile(tmp, JSON.stringify(idx), 'utf-8');
     await fs.rename(tmp, path.join(durableDir, DURABLE_INDEX_FILENAME));
 };
+/**
+ * Overlay this run's staged durable ParsedFile chunks onto the live store,
+ * then prune the live tree to `keepKeys`. Live chunks this run did not rewrite
+ * (other branches, unused hashes) stay until prune. No-op overlay when the
+ * staged dir is missing.
+ */
+export const mergeStagedDurableParsedFileStore = async (liveStoragePath, stagedStoragePath, version, keepKeys) => {
+    const liveDir = getDurableParsedFileDir(liveStoragePath);
+    if (stagedStoragePath === liveStoragePath) {
+        await pruneAndSaveDurableParsedFileStore(liveDir, version, keepKeys);
+        return;
+    }
+    const stagedDir = getDurableParsedFileDir(stagedStoragePath);
+    await fs.mkdir(liveDir, { recursive: true });
+    let stagedEntries = [];
+    try {
+        stagedEntries = await fs.readdir(stagedDir);
+    }
+    catch {
+        await pruneAndSaveDurableParsedFileStore(liveDir, version, keepKeys);
+        return;
+    }
+    for (const name of stagedEntries) {
+        if (name === DURABLE_INDEX_FILENAME)
+            continue;
+        const from = path.join(stagedDir, name);
+        const to = path.join(liveDir, name);
+        await replaceDurableChunkDir(from, to);
+    }
+    await pruneAndSaveDurableParsedFileStore(liveDir, version, keepKeys);
+};
+/** Move `from` onto `to` without deleting `to` until the new tree is in place. */
+const replaceDurableChunkDir = async (from, to) => {
+    try {
+        await fs.rename(from, to);
+        return;
+    }
+    catch {
+        /* dest exists, or the rename is cross-device */
+    }
+    const backup = `${to}.replacing`;
+    await fs.rm(backup, { recursive: true, force: true });
+    let backedUp = false;
+    try {
+        await fs.rename(to, backup);
+        backedUp = true;
+    }
+    catch {
+        /* dest was missing */
+    }
+    try {
+        try {
+            await fs.rename(from, to);
+        }
+        catch {
+            await fs.cp(from, to, { recursive: true });
+            await fs.rm(from, { recursive: true, force: true });
+        }
+    }
+    catch (err) {
+        if (backedUp) {
+            await fs.rm(to, { recursive: true, force: true }).catch(() => { });
+            await fs.rename(backup, to).catch(() => { });
+        }
+        throw err;
+    }
+    if (backedUp) {
+        await fs.rm(backup, { recursive: true, force: true });
+    }
+};

package/dist/types/pipeline.d.ts

@@ -52,6 +52,8 @@ export interface PipelineResult {
     usedWorkerPool: boolean;
     /** Files actually dispatched to parser workers after parse-cache lookup. */
     reparsedFileCount: number;
+    /** Files restored from parse-cache chunks without parser-worker dispatch. */
+    parseCacheHitFileCount?: number;
     /** Files omitted from scope-resolution while the rest of analysis continued. */
     scopeExtractionFailures: readonly string[];
     /** Files scope resolution could not inspect because their parser was unavailable. */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.11-rc.47",
+  "version": "1.6.11-rc.48",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",
@@ -40,6 +40,7 @@
   ],
   "scripts": {
     "build": "node scripts/build.js",
+    "build:web": "node scripts/build.js --web",
     "serve": "tsx src/cli/index.ts serve",
     "dev": "tsx watch src/cli/index.ts",
     "test": "vitest run",
@@ -52,7 +53,7 @@
     "postinstall": "node scripts/build-tree-sitter-grammars.cjs",
     "assert-publish-coverage": "node scripts/assert-publish-grammar-coverage.cjs",
     "prepare": "node scripts/build.js",
-    "prepack": "node scripts/assert-publish-grammar-coverage.cjs && node scripts/build.js",
+    "prepack": "node scripts/assert-publish-grammar-coverage.cjs && node scripts/build.js --web && node scripts/assert-web-assets.mjs web",
     "version": "node scripts/sync-plugin-manifests.mjs"
   },
   "dependencies": {

package/scripts/assert-web-assets.mjs

@@ -0,0 +1,35 @@
+#!/usr/bin/env node
+import fs from 'node:fs';
+import path from 'node:path';
+
+const webDir = path.resolve(process.argv[2] ?? 'web');
+const indexPath = path.join(webDir, 'index.html');
+
+let html;
+try {
+  html = fs.readFileSync(indexPath, 'utf8');
+} catch (err) {
+  if (err?.code === 'ENOENT') {
+    console.error(`[web-assets] missing ${indexPath}`);
+    process.exit(1);
+  }
+  throw err;
+}
+const localRefs = [...html.matchAll(/(?:src|href)=["']([^"'#]+)["']/g)]
+  .map((match) => match[1])
+  .filter((ref) => !/^(?:[a-z]+:|\/\/|data:)/i.test(ref))
+  .map((ref) => ref.split(/[?#]/, 1)[0].replace(/^\/+/, ''));
+const assetRefs = localRefs.filter((ref) => ref.startsWith('assets/'));
+
+if (assetRefs.length === 0) {
+  console.error(`[web-assets] ${indexPath} references no assets`);
+  process.exit(1);
+}
+
+const missing = assetRefs.filter((ref) => !fs.existsSync(path.join(webDir, ref)));
+if (missing.length > 0) {
+  console.error(`[web-assets] ${indexPath} references missing assets:\n${missing.join('\n')}`);
+  process.exit(1);
+}
+
+console.log(`[web-assets] verified index.html and ${assetRefs.length} referenced asset(s)`);

package/scripts/build-web.js

@@ -0,0 +1,72 @@
+import { execSync } from 'node:child_process';
+import fs from 'node:fs';
+import path from 'node:path';
+
+export function shouldBuildWeb(argv = process.argv, env = process.env) {
+  return argv.includes('--web') || env.GITNEXUS_BUILD_WEB === '1';
+}
+
+export function shouldPreserveWebOutput(env = process.env) {
+  return (
+    env.npm_lifecycle_event === 'prepare' &&
+    (env.npm_command === 'pack' || env.npm_command === 'publish')
+  );
+}
+
+/** Build and copy the web UI when `--web` / GITNEXUS_BUILD_WEB=1 is set. */
+export function runWebBuild({
+  root,
+  dist,
+  timeoutMs,
+  argv = process.argv,
+  env = process.env,
+  fsImpl = fs,
+  exec = execSync,
+}) {
+  const webRoot = path.resolve(root, '..', 'gitnexus-web');
+  const webDest = path.join(dist, '..', 'web');
+
+  if (!shouldBuildWeb(argv, env)) {
+    if (shouldPreserveWebOutput(env)) {
+      console.log('[build] preserving prepack web UI during npm prepare');
+    } else {
+      fsImpl.rmSync(webDest, { recursive: true, force: true });
+      console.log(
+        '[build] skipping web UI and removed stale output ' +
+          '(pass --web or set GITNEXUS_BUILD_WEB=1 to include it)',
+      );
+    }
+    return { status: 'skipped', webDest };
+  }
+
+  if (!fsImpl.existsSync(path.join(webRoot, 'package.json'))) {
+    throw new Error(
+      `[build] web UI requested, but gitnexus-web was not found at ${webRoot}. ` +
+        'Run this command from the complete monorepo checkout.',
+    );
+  }
+
+  console.log('[build] building gitnexus-web…');
+  if (!fsImpl.existsSync(path.join(webRoot, 'node_modules'))) {
+    // Deliberately untimed: this is a full second install, and killing it
+    // partway through leaves a broken tree and a misleading ETIMEDOUT.
+    // CI should install gitnexus-web itself (cached, its own step) so this
+    // fallback only fires for a local `npm pack` / `npm publish`.
+    console.log('[build] installing gitnexus-web dependencies (no local node_modules)…');
+    // String form uses the platform shell (cmd.exe / sh) so `npm` resolves to
+    // npm.cmd on Windows. execFileSync('npm') / execFileSync('npm.cmd')
+    // without a shell fails on Windows.
+    exec('npm ci', { cwd: webRoot, stdio: 'inherit' });
+  }
+  exec('npm run build', { cwd: webRoot, stdio: 'inherit', timeout: timeoutMs });
+
+  const builtIndex = path.join(webRoot, 'dist', 'index.html');
+  if (!fsImpl.existsSync(builtIndex)) {
+    throw new Error(`[build] gitnexus-web build completed without ${builtIndex}`);
+  }
+
+  fsImpl.rmSync(webDest, { recursive: true, force: true });
+  fsImpl.cpSync(path.join(webRoot, 'dist'), webDest, { recursive: true });
+  console.log('[build] copied web UI → gitnexus/web/');
+  return { status: 'built', webDest };
+}

package/scripts/build.js

@@ -8,17 +8,18 @@
  *  3. Copy gitnexus-shared/dist → dist/_shared
  *  4. Rewrite bare 'gitnexus-shared' specifiers → relative paths
  */
-import { execSync } from 'node:child_process';
+import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
 import { fileURLToPath } from 'node:url';
+import { runWebBuild } from './build-web.js';
 
 const __dirname = path.dirname(fileURLToPath(import.meta.url));
 const ROOT = path.resolve(__dirname, '..');
 const SHARED_ROOT = path.resolve(ROOT, '..', 'gitnexus-shared');
 const DIST = path.join(ROOT, 'dist');
 const SHARED_DEST = path.join(DIST, '_shared');
-const DEFAULT_BUILD_TIMEOUT_MS = 300_000;
+const DEFAULT_BUILD_TIMEOUT_MS = 600_000;
 
 function getBuildTimeoutMs() {
   const raw = process.env.GITNEXUS_BUILD_TIMEOUT_MS;
@@ -51,17 +52,29 @@ if (!fs.existsSync(SHARED_ROOT)) {
   process.exit(1);
 }
 
+// Launch tsc as `node typescript/lib/tsc.js` on every OS. The `.bin/tsc` /
+// `tsc.cmd` shims are Windows-only wrappers; `execFileSync` cannot spawn a
+// `.cmd` without a shell, and a separate `npm ci` in gitnexus-shared pulls
+// TypeScript 7 optional platform packages (7+ minutes in CI).
+const tscJs = path.join(ROOT, 'node_modules', 'typescript', 'lib', 'tsc.js');
+if (!fs.existsSync(tscJs)) {
+  console.error(
+    `[build] missing ${tscJs}. Install gitnexus dependencies first (npm ci in gitnexus/).`,
+  );
+  process.exit(1);
+}
+
+function runTsc(cwd) {
+  execFileSync(process.execPath, [tscJs], { cwd, stdio: 'inherit', timeout: BUILD_TIMEOUT_MS });
+}
+
 // ── 1. Build gitnexus-shared ───────────────────────────────────────
 console.log('[build] compiling gitnexus-shared…');
-const tscCmd =
-  process.platform === 'win32'
-    ? path.join('node_modules', '.bin', 'tsc.cmd')
-    : path.join('node_modules', '.bin', 'tsc');
-execSync(tscCmd, { cwd: SHARED_ROOT, stdio: 'inherit', timeout: BUILD_TIMEOUT_MS });
+runTsc(SHARED_ROOT);
 
 // ── 2. Build gitnexus ──────────────────────────────────────────────
 console.log('[build] compiling gitnexus…');
-execSync(tscCmd, { cwd: ROOT, stdio: 'inherit', timeout: BUILD_TIMEOUT_MS });
+runTsc(ROOT);
 
 // ── 3. Copy shared dist ────────────────────────────────────────────
 console.log('[build] copying shared module into dist/_shared…');
@@ -104,26 +117,16 @@ walk(DIST, ['.js', '.d.ts'], rewriteFile);
 
 // ── 5. Make CLI entry executable ────────────────────────────────────
 const cliEntry = path.join(DIST, 'cli', 'index.js');
-if (fs.existsSync(cliEntry)) fs.chmodSync(cliEntry, 0o755);
-
-// ── 6. Build & copy web UI ──────────────────────────────────────────
-const WEB_ROOT = path.resolve(ROOT, '..', 'gitnexus-web');
-const WEB_DEST = path.join(DIST, '..', 'web');
-
-if (fs.existsSync(path.join(WEB_ROOT, 'package.json'))) {
-  console.log('[build] building gitnexus-web…');
-  if (!fs.existsSync(path.join(WEB_ROOT, 'node_modules'))) {
-    console.log('[build] installing gitnexus-web dependencies…');
-    execSync('npm ci', { cwd: WEB_ROOT, stdio: 'inherit', timeout: BUILD_TIMEOUT_MS });
-  }
-  execSync('npm run build', { cwd: WEB_ROOT, stdio: 'inherit', timeout: BUILD_TIMEOUT_MS });
-
-  // Copy dist → gitnexus/web/ (shipped in the npm package)
-  fs.rmSync(WEB_DEST, { recursive: true, force: true });
-  fs.cpSync(path.join(WEB_ROOT, 'dist'), WEB_DEST, { recursive: true });
-  console.log('[build] copied web UI → gitnexus/web/');
-} else {
-  console.log('[build] skipping web UI (gitnexus-web not found)');
+if (process.platform !== 'win32' && fs.existsSync(cliEntry)) {
+  fs.chmodSync(cliEntry, 0o755);
 }
 
+// ── 6. Build & copy web UI (opt-in) ─────────────────────────────────
+// Web UI is a separate package and is only required in the published
+// tarball, so it is built by `prepack --web`, not by `prepare`. Serve
+// falls back to the landing page when web/ is absent. CLI-only builds
+// delete stale web/ except during npm pack/publish prepare, which must
+// keep the prepack output.
+runWebBuild({ root: ROOT, dist: DIST, timeoutMs: BUILD_TIMEOUT_MS });
+
 console.log(`[build] done — rewrote ${rewritten} files.`);