gitnexus 1.6.5-rc.3 → 1.6.5-rc.30

package/dist/_shared/scope-resolution/method-dispatch-index.d.ts

@@ -36,10 +36,26 @@ export interface MethodDispatchIndex {
     readonly mroByOwnerDefId: ReadonlyMap<DefId, readonly DefId[]>;
     /** Interfaces / traits → classes that implement them. */
     readonly implsByInterfaceDefId: ReadonlyMap<DefId, readonly DefId[]>;
+    /**
+     * Optional parallel MRO view that EXCLUDES mixin-like augmentation
+     * (e.g., PHP traits). Populated only when the input supplies
+     * `computeExtendsOnlyMro`. Used by the super-branch dispatch in
+     * `receiver-bound-calls` so that `parent::method()` walks the
+     * inheritance chain only, not the trait-augmented one. Undefined for
+     * languages without mixin-like semantics — callers should fall back
+     * to `mroFor` when this is missing.
+     */
+    readonly extendsOnlyMroByOwnerDefId?: ReadonlyMap<DefId, readonly DefId[]>;
     /** `mroByOwnerDefId.get`, with an empty frozen array on miss. */
     mroFor(ownerDefId: DefId): readonly DefId[];
     /** `implsByInterfaceDefId.get`, with an empty frozen array on miss. */
     implementorsOf(interfaceDefId: DefId): readonly DefId[];
+    /**
+     * `extendsOnlyMroByOwnerDefId.get`, with an empty frozen array on miss.
+     * Undefined when `extendsOnlyMroByOwnerDefId` was not populated; callers
+     * should treat this as equivalent to `mroFor` for non-mixin languages.
+     */
+    readonly extendsOnlyMroFor?: (ownerDefId: DefId) => readonly DefId[];
 }
 export interface MethodDispatchInput {
     /**
@@ -75,6 +91,16 @@ export interface MethodDispatchInput {
      * write-wins policy and fires at most once per unique owner.
      */
     readonly implementsOf: (ownerDefId: DefId) => readonly DefId[];
+    /**
+     * Optional: return the EXTENDS-only ancestor chain for `ownerDefId`,
+     * excluding the owner itself AND any mixin-like augmentation (e.g.,
+     * PHP traits). Languages without mixin semantics leave this undefined
+     * and the index's `extendsOnlyMroByOwnerDefId` stays unpopulated.
+     *
+     * Same contract as `computeMro`: pure, deterministic, `[]` on no parents.
+     * Called at most once per unique owner (first-write-wins).
+     */
+    readonly computeExtendsOnlyMro?: (ownerDefId: DefId) => readonly DefId[];
 }
 export declare function buildMethodDispatchIndex(input: MethodDispatchInput): MethodDispatchIndex;
 //# sourceMappingURL=method-dispatch-index.d.ts.map

package/dist/_shared/scope-resolution/method-dispatch-index.d.ts.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/method-dispatch-index.js

@@ -30,6 +30,9 @@
 // ─── Builder ────────────────────────────────────────────────────────────────
 export function buildMethodDispatchIndex(input) {
     const mroByOwnerDefId = new Map();
+    const extendsOnlyByOwnerDefId = input.computeExtendsOnlyMro
+        ? new Map()
+        : undefined;
     const implsBuilding = new Map();
     const implsSeen = new Map();
     for (const ownerId of input.owners) {
@@ -39,6 +42,12 @@ export function buildMethodDispatchIndex(input) {
             const chain = input.computeMro(ownerId);
             mroByOwnerDefId.set(ownerId, Object.freeze(chain.slice()));
         }
+        if (input.computeExtendsOnlyMro !== undefined &&
+            extendsOnlyByOwnerDefId !== undefined &&
+            !extendsOnlyByOwnerDefId.has(ownerId)) {
+            const extOnly = input.computeExtendsOnlyMro(ownerId);
+            extendsOnlyByOwnerDefId.set(ownerId, Object.freeze(extOnly.slice()));
+        }
         for (const ifaceId of input.implementsOf(ownerId)) {
             let seen = implsSeen.get(ifaceId);
             if (seen === undefined) {
@@ -60,12 +69,12 @@ export function buildMethodDispatchIndex(input) {
     for (const [ifaceId, owners] of implsBuilding) {
         implsByInterfaceDefId.set(ifaceId, Object.freeze(owners.slice()));
     }
-    return wrapIndex(mroByOwnerDefId, implsByInterfaceDefId);
+    return wrapIndex(mroByOwnerDefId, implsByInterfaceDefId, extendsOnlyByOwnerDefId);
 }
 // ─── Internal ───────────────────────────────────────────────────────────────
 const EMPTY = Object.freeze([]);
-function wrapIndex(mroByOwnerDefId, implsByInterfaceDefId) {
-    return {
+function wrapIndex(mroByOwnerDefId, implsByInterfaceDefId, extendsOnlyMroByOwnerDefId) {
+    const base = {
         mroByOwnerDefId,
         implsByInterfaceDefId,
         mroFor(ownerDefId) {
@@ -75,5 +84,15 @@ function wrapIndex(mroByOwnerDefId, implsByInterfaceDefId) {
             return implsByInterfaceDefId.get(interfaceDefId) ?? EMPTY;
         },
     };
+    if (extendsOnlyMroByOwnerDefId !== undefined) {
+        return {
+            ...base,
+            extendsOnlyMroByOwnerDefId,
+            extendsOnlyMroFor(ownerDefId) {
+                return extendsOnlyMroByOwnerDefId.get(ownerDefId) ?? EMPTY;
+            },
+        };
+    }
+    return base;
 }
 //# sourceMappingURL=method-dispatch-index.js.map

package/dist/_shared/scope-resolution/method-dispatch-index.js.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/registries/lookup-core.js

@@ -299,14 +299,31 @@ function applyArityFilter(callsite, perCandidate, ctx) {
         return;
     }
     let anyCompatible = false;
+    let anyUnknown = false;
     for (const state of perCandidate.values()) {
         const verdict = arityFn(callsite, state.def);
         state.signals.arityVerdict = verdict;
         if (verdict === 'compatible')
             anyCompatible = true;
+        else if (verdict === 'unknown')
+            anyUnknown = true;
     }
-    if (!anyCompatible)
+    // When ALL candidates are 'incompatible' (none compatible, none unknown),
+    // the call is genuinely arity-broken — drop every candidate so the
+    // registry returns no resolution. This matches the PHP variadic case
+    // f(int $req, ...$rest) called with zero args: every candidate definitively
+    // rejects, and emitting an edge to a definitively-rejected callable is
+    // a false positive. When some candidates are 'unknown' (missing metadata),
+    // keep the set so downstream evidence can break the tie — that's the
+    // original safety-fallback behavior.
+    if (!anyCompatible) {
+        if (!anyUnknown) {
+            for (const defId of perCandidate.keys()) {
+                perCandidate.delete(defId);
+            }
+        }
         return;
+    }
     // Filter: when at least one compatible candidate exists, drop incompatibles.
     for (const [defId, state] of perCandidate) {
         if (state.signals.arityVerdict === 'incompatible') {

package/dist/_shared/scope-resolution/registries/lookup-core.js.map

@@ -1 +1 @@
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package/dist/cli/ai-context.d.ts

@@ -17,6 +17,7 @@ interface RepoStats {
 export interface AIContextOptions {
     skipAgentsMd?: boolean;
     noStats?: boolean;
+    skipSkills?: boolean;
 }
 /**
  * Generate AI context files after indexing

package/dist/cli/ai-context.js

@@ -68,20 +68,31 @@ async function findGroupsContainingRegistryName(registryName) {
     }
     return hits;
 }
-function generateGitNexusContent(projectName, stats, generatedSkills, groupNames, noStats) {
+function generateGitNexusContent(projectName, stats, generatedSkills, groupNames, noStats, skipSkills) {
     const generatedRows = generatedSkills && generatedSkills.length > 0
         ? generatedSkills
             .map((s) => `| Work in the ${s.label} area (${s.symbolCount} symbols) | \`.claude/skills/generated/${s.name}/SKILL.md\` |`)
             .join('\n')
         : '';
-    const skillsTable = `| Task | Read this skill file |
-|------|---------------------|
-| Understand architecture / "How does X work?" | \`.claude/skills/gitnexus/gitnexus-exploring/SKILL.md\` |
+    // Standard skill rows reference files installed by installSkills(). When
+    // --skip-skills suppresses that install, these rows must be omitted — else
+    // AGENTS.md/CLAUDE.md would direct agents to read files that don't exist.
+    // Community skills (generatedRows) live in .claude/skills/generated/ and
+    // are independent of --skip-skills, so they remain when present.
+    const standardSkillsRows = skipSkills
+        ? ''
+        : `| Understand architecture / "How does X work?" | \`.claude/skills/gitnexus/gitnexus-exploring/SKILL.md\` |
 | Blast radius / "What breaks if I change X?" | \`.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md\` |
 | Trace bugs / "Why is X failing?" | \`.claude/skills/gitnexus/gitnexus-debugging/SKILL.md\` |
 | Rename / extract / split / refactor | \`.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md\` |
 | Tools, resources, schema reference | \`.claude/skills/gitnexus/gitnexus-guide/SKILL.md\` |
-| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus/gitnexus-cli/SKILL.md\` |${generatedRows ? '\n' + generatedRows : ''}`;
+| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus/gitnexus-cli/SKILL.md\` |`;
+    const tableBody = [standardSkillsRows, generatedRows].filter(Boolean).join('\n');
+    const skillsTable = tableBody
+        ? `| Task | Read this skill file |
+|------|---------------------|
+${tableBody}`
+        : '';
     return `${GITNEXUS_START_MARKER}
 # GitNexus — Code Intelligence
 
@@ -119,11 +130,13 @@ ${groupNames && groupNames.length > 0
 This repository is listed under GitNexus **group(s): ${groupNames.join(', ')}** (see \`~/.gitnexus/groups/\`). For cross-repo analysis, use MCP tools \`impact\`, \`query\`, and \`context\` with \`repo\` set to \`@<groupName>\` or \`@<groupName>/<memberPath>\` (paths match keys in that group’s \`group.yaml\`). Use \`group_list\` / \`group_sync\` for membership and sync. From the terminal: \`npx gitnexus group list\`, \`npx gitnexus group sync <name>\`, \`npx gitnexus group impact <name> --target <symbol> --repo <group-path>\`.
 
 `
-        : ''}## CLI
+        : ''}${skillsTable
+        ? `## CLI
 
 ${skillsTable}
 
-${GITNEXUS_END_MARKER}`;
+`
+        : ''}${GITNEXUS_END_MARKER}`;
 }
 /**
  * Check if a file exists
@@ -143,7 +156,7 @@ async function fileExists(filePath) {
  * - If file exists without GitNexus section: append
  * - If file exists with GitNexus section: replace that section
  */
-async function upsertGitNexusSection(filePath, content) {
+async function upsertGitNexusSection(filePath, content, projectName, stats) {
     const exists = await fileExists(filePath);
     if (!exists) {
         await fs.writeFile(filePath, content, 'utf-8');
@@ -159,7 +172,43 @@ async function upsertGitNexusSection(filePath, content) {
     const startIdx = findSectionMarkerIndex(existingContent, GITNEXUS_START_MARKER);
     const endIdx = findSectionMarkerIndex(existingContent, GITNEXUS_END_MARKER, startIdx === -1 ? 0 : startIdx);
     if (startIdx !== -1 && endIdx !== -1 && endIdx > startIdx) {
-        // Replace existing section
+        const existingSection = existingContent.substring(startIdx, endIdx + GITNEXUS_END_MARKER.length);
+        // If the existing section contains <!-- gitnexus:keep -->, preserve the user's
+        // custom layout and only update the stats line (node/edge/flow counts).
+        // This lets teams trim the verbose default template to a lean format without
+        // having it overwritten on every `gitnexus analyze`.
+        //
+        // Note: the keep-marker check operates on `existingSection` (the substring
+        // between valid section markers identified by findSectionMarkerIndex), so
+        // a keep marker in user prose OUTSIDE the GitNexus block has no effect.
+        if (existingSection.includes('<!-- gitnexus:keep -->')) {
+            // Build the new stats line from the caller-provided values directly.
+            // We do NOT re-extract from `content` because:
+            //   (a) first-bold extraction is fragile if the template evolves
+            //   (b) the parenthesized-text fallback can match unrelated tuples
+            //       like `({target: "symbolName", direction: "upstream"})`
+            //       when noStats is set
+            // Passing projectName + stats explicitly makes the contract obvious.
+            // noStats controls template generation, not keep-section stat updates — the user opted into a stats line by keeping it.
+            const newStatsInner = `${stats.nodes || 0} symbols, ${stats.edges || 0} relationships, ${stats.processes || 0} execution flows`;
+            const statsLine = `Indexed as **${projectName}** (${newStatsInner})`;
+            // Match either canonical phrasing at line start (`^` with `m` flag) so we
+            // cannot replace prose embedded mid-paragraph. Deliberately no `$`: text
+            // after the closing `)` on the same line (e.g. ". MCP tools.") stays intact.
+            const statsPattern = /^(?:Indexed as|indexed by GitNexus as) \*\*[^*]+\*\* \([^)]+\)/m;
+            if (statsPattern.test(existingSection)) {
+                const updatedSection = existingSection.replace(statsPattern, statsLine);
+                const before = existingContent.substring(0, startIdx);
+                const after = existingContent.substring(endIdx + GITNEXUS_END_MARKER.length);
+                await fs.writeFile(filePath, (before + updatedSection + after).trim() + '\n', 'utf-8');
+                return 'updated';
+            }
+            // Keep marker present but no stats line matched. Section is preserved
+            // unchanged on disk; return a distinct status so callers/CLI output
+            // don't mis-report this as 'updated' (which would imply a write).
+            return 'preserved';
+        }
+        // No keep marker — replace existing section with full verbose content
         const before = existingContent.substring(0, startIdx);
         const after = existingContent.substring(endIdx + GITNEXUS_END_MARKER.length);
         const newContent = before + content + after;
@@ -246,26 +295,31 @@ Use GitNexus tools to accomplish this task.
  */
 export async function generateAIContextFiles(repoPath, _storagePath, projectName, stats, generatedSkills, options) {
     const groupNames = await findGroupsContainingRegistryName(projectName);
-    const content = generateGitNexusContent(projectName, stats, generatedSkills, groupNames, options?.noStats);
+    const content = generateGitNexusContent(projectName, stats, generatedSkills, groupNames, options?.noStats, options?.skipSkills);
     const createdFiles = [];
     if (!options?.skipAgentsMd) {
         // Create AGENTS.md (standard for Cursor, Windsurf, OpenCode, Cline, etc.)
         const agentsPath = path.join(repoPath, 'AGENTS.md');
-        const agentsResult = await upsertGitNexusSection(agentsPath, content);
+        const agentsResult = await upsertGitNexusSection(agentsPath, content, projectName, stats);
         createdFiles.push(`AGENTS.md (${agentsResult})`);
         // Create CLAUDE.md (for Claude Code)
         const claudePath = path.join(repoPath, 'CLAUDE.md');
-        const claudeResult = await upsertGitNexusSection(claudePath, content);
+        const claudeResult = await upsertGitNexusSection(claudePath, content, projectName, stats);
         createdFiles.push(`CLAUDE.md (${claudeResult})`);
     }
     else {
         createdFiles.push('AGENTS.md (skipped via --skip-agents-md)');
         createdFiles.push('CLAUDE.md (skipped via --skip-agents-md)');
     }
-    // Install skills to .claude/skills/gitnexus/
-    const installedSkills = await installSkills(repoPath);
-    if (installedSkills.length > 0) {
-        createdFiles.push(`.claude/skills/gitnexus/ (${installedSkills.length} skills)`);
+    // Install skills to .claude/skills/gitnexus/ (unless --skip-skills)
+    if (!options?.skipSkills) {
+        const installedSkills = await installSkills(repoPath);
+        if (installedSkills.length > 0) {
+            createdFiles.push(`.claude/skills/gitnexus/ (${installedSkills.length} skills)`);
+        }
+    }
+    else {
+        createdFiles.push('.claude/skills/gitnexus/ (skipped via --skip-skills)');
     }
     return { files: createdFiles };
 }

package/dist/cli/analyze.d.ts

@@ -29,6 +29,10 @@ export interface AnalyzeOptions {
     skipAgentsMd?: boolean;
     /** Omit volatile symbol/relationship counts from AGENTS.md and CLAUDE.md. */
     noStats?: boolean;
+    /** Skip installing standard GitNexus skill files to .claude/skills/gitnexus/. */
+    skipSkills?: boolean;
+    /** Pure index mode: skip all file injection (AGENTS.md, CLAUDE.md, skills). */
+    indexOnly?: boolean;
     /** Index the folder even when no .git directory is present. */
     skipGit?: boolean;
     /**
@@ -59,4 +63,18 @@ export interface AnalyzeOptions {
     embeddingSubBatchSize?: string;
     embeddingDevice?: string;
 }
+/**
+ * Whether the post-index skill step should run.
+ *
+ * The gated block does two things in sequence: (1) generates the community
+ * skill files from `--skills`, and (2) re-runs `generateAIContextFiles` so
+ * AGENTS.md/CLAUDE.md can reference the freshly written skills. Both are
+ * suppressed together — `--index-only` drops the entire step, not just the
+ * community-skill write. Name retained for the test contract; see call site
+ * in `analyzeCommand` for the AGENTS.md/CLAUDE.md re-generation it also gates.
+ *
+ * Kept as a pure helper so the `--index-only --skills` contract is unit-tested
+ * without booting the full analyze pipeline (#742 review).
+ */
+export declare const shouldGenerateCommunitySkillFiles: (options: Pick<AnalyzeOptions, "skills" | "indexOnly"> | undefined, pipelineResult: unknown) => boolean;
 export declare const analyzeCommand: (inputPath?: string, options?: AnalyzeOptions) => Promise<void>;

package/dist/cli/analyze.js

@@ -86,6 +86,20 @@ function ensureHeap() {
     }
     return true;
 }
+/**
+ * Whether the post-index skill step should run.
+ *
+ * The gated block does two things in sequence: (1) generates the community
+ * skill files from `--skills`, and (2) re-runs `generateAIContextFiles` so
+ * AGENTS.md/CLAUDE.md can reference the freshly written skills. Both are
+ * suppressed together — `--index-only` drops the entire step, not just the
+ * community-skill write. Name retained for the test contract; see call site
+ * in `analyzeCommand` for the AGENTS.md/CLAUDE.md re-generation it also gates.
+ *
+ * Kept as a pure helper so the `--index-only --skills` contract is unit-tested
+ * without booting the full analyze pipeline (#742 review).
+ */
+export const shouldGenerateCommunitySkillFiles = (options, pipelineResult) => Boolean(options?.skills && pipelineResult && !options?.indexOnly);
 export const analyzeCommand = async (inputPath, options) => {
     if (ensureHeap())
         return;
@@ -151,6 +165,15 @@ export const analyzeCommand = async (inputPath, options) => {
         process.env.GITNEXUS_EMBEDDING_DEVICE = options.embeddingDevice;
     }
     console.log('\n  GitNexus Analyzer\n');
+    // `--index-only` is the stronger contract — it suppresses every form of file
+    // injection, including community skill writes that `--skills` would normally
+    // produce. Surface the override explicitly so users don't wonder why a
+    // pipeline re-index ran but no skill files appeared. The pipeline still
+    // re-runs (see `force: options?.force || options?.skills` below); the warning
+    // is purely about the dropped post-index write step.
+    if (options?.indexOnly && options?.skills) {
+        console.log('  Note: --index-only overrides --skills; community skill files will not be written.\n');
+    }
     let repoPath;
     if (inputPath) {
         repoPath = path.resolve(inputPath);
@@ -285,6 +308,9 @@ export const analyzeCommand = async (inputPath, options) => {
     const t0 = Date.now();
     // ── Run shared analysis orchestrator ───────────────────────────────
     try {
+        const skipAll = options?.indexOnly;
+        const skipAgentsMd = skipAll || options?.skipAgentsMd;
+        const skipSkills = skipAll || options?.skipSkills;
         const result = await runFullAnalysis(repoPath, {
             // Pipeline re-index — OR'd with --skills because skill generation
             // needs a fresh pipelineResult. Has no bearing on the registry
@@ -294,7 +320,8 @@ export const analyzeCommand = async (inputPath, options) => {
             embeddingsNodeLimit,
             dropEmbeddings: options?.dropEmbeddings,
             skipGit: options?.skipGit,
-            skipAgentsMd: options?.skipAgentsMd,
+            skipAgentsMd,
+            skipSkills,
             noStats: options?.noStats,
             registryName: options?.name,
             // Registry-collision bypass — its own CLI flag, intentionally NOT
@@ -335,8 +362,10 @@ export const analyzeCommand = async (inputPath, options) => {
         // exit code and an actionable error instead of being mistaken for
         // a healthy index.
         await assertAnalysisFinalized(repoPath);
-        // Skill generation (CLI-only, uses pipeline result from analysis)
-        if (options?.skills && result.pipelineResult) {
+        // Skill generation (CLI-only, uses pipeline result from analysis).
+        // Gated so `--index-only --skills` skips community skill writes too
+        // (`shouldGenerateCommunitySkillFiles` — see unit test).
+        if (shouldGenerateCommunitySkillFiles(options, result.pipelineResult)) {
             updateBar(99, 'Generating skill files...');
             try {
                 const { generateSkillFiles } = await import('./skill-gen.js');
@@ -364,7 +393,7 @@ export const analyzeCommand = async (inputPath, options) => {
                         communities: s.communities,
                         clusters: aggregatedClusterCount,
                         processes: s.processes,
-                    }, skillResult.skills, { skipAgentsMd: options?.skipAgentsMd, noStats: options?.noStats });
+                    }, skillResult.skills, { skipAgentsMd, skipSkills, noStats: options?.noStats });
                 }
             }
             catch {

package/dist/cli/index.js

@@ -21,9 +21,14 @@ program
     'Optional [limit] overrides the 50,000-node safety cap; pass 0 to disable the cap entirely.')
     .option('--drop-embeddings', 'Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` ' +
     'preserves any embeddings already present in the index.')
-    .option('--skills', 'Generate repo-specific skill files from detected communities')
+    .option('--skills', 'Generate repo-specific skill files from detected communities ' +
+    '(no-op when --index-only is also set).')
     .option('--skip-agents-md', 'Skip updating the gitnexus section in AGENTS.md and CLAUDE.md')
     .option('--no-stats', 'Omit volatile file/symbol counts from AGENTS.md and CLAUDE.md')
+    .option('--skip-skills', 'Skip installing standard GitNexus skill files under .claude/skills/gitnexus/. ' +
+    'Does not suppress community skills from --skills (those use .claude/skills/generated/). ' +
+    'Use --index-only to skip all AI-context file injection.')
+    .option('--index-only', 'Pure index mode: skip all file injection (AGENTS.md, CLAUDE.md, skills)')
     .option('--skip-git', 'Treat the provided path/cwd as the index root and skip parent git-root discovery')
     .option('--name <alias>', 'Register this repo under a custom name in ~/.gitnexus/registry.json ' +
     '(disambiguates repos whose paths share a basename, e.g. two different .../app folders)')
@@ -98,6 +103,8 @@ program
     .option('--reasoning-model', 'Mark deployment as reasoning model (o1/o3/o4-mini) — strips temperature, uses max_completion_tokens')
     .option('--no-reasoning-model', 'Disable reasoning model mode (overrides saved config)')
     .option('--concurrency <n>', 'Parallel LLM calls (default: 3)', '3')
+    .option('--timeout <seconds>', 'Per-attempt LLM request timeout in seconds (default: 60)')
+    .option('--retries <n>', 'Max LLM retry attempts per request (default: 3)')
     .option('--gist', 'Publish wiki as a public GitHub Gist after generation')
     .option('-v, --verbose', 'Enable verbose output (show LLM commands and responses)')
     .option('--review', 'Stop after grouping to review module structure before generating pages')

package/dist/cli/setup.js

@@ -308,6 +308,12 @@ async function installClaudeCodeHooks(result) {
         catch {
             // Script not found in source — skip
         }
+        try {
+            await fs.copyFile(path.join(pluginHooksPath, 'hook-lock.cjs'), path.join(destHooksDir, 'hook-lock.cjs'));
+        }
+        catch {
+            // Helper not found in source — skip
+        }
         const hookPath = path.join(destHooksDir, 'gitnexus-hook.cjs').replace(/\\/g, '/');
         // Escape backslashes FIRST, then quotes (CodeQL js/incomplete-sanitization).
         // The previous shape `replace(/"/g, '\\"')` alone would let `path\with"quote`

package/dist/cli/wiki.d.ts

@@ -17,5 +17,7 @@ export interface WikiCommandOptions {
     provider?: LLMProvider;
     verbose?: boolean;
     review?: boolean;
+    timeout?: string;
+    retries?: string;
 }
 export declare const wikiCommand: (inputPath?: string, options?: WikiCommandOptions) => Promise<void>;

package/dist/cli/wiki.js

@@ -304,6 +304,17 @@ export const wikiCommand = async (inputPath, options) => {
             }
         }
     }
+    // ── Apply per-run overrides not saved to config ────────────────────
+    if (options?.timeout) {
+        const secs = parseInt(options.timeout, 10);
+        if (!isNaN(secs) && secs > 0)
+            llmConfig.requestTimeoutMs = secs * 1000;
+    }
+    if (options?.retries) {
+        const n = parseInt(options.retries, 10);
+        if (!isNaN(n) && n > 0)
+            llmConfig.maxAttempts = n;
+    }
     // ── Setup progress bar with elapsed timer ──────────────────────────
     const bar = new cliProgress.SingleBar({
         format: '  {bar} {percentage}% | {phase}',

package/dist/core/augmentation/engine.js

@@ -76,6 +76,9 @@ async function findRepoForCwd(cwd) {
 export async function augment(pattern, cwd) {
     if (!pattern || pattern.length < 3)
         return '';
+    const patternFirstWord = pattern.trim().replace(/'/g, "''").split(/\s+/)[0];
+    if (!patternFirstWord || patternFirstWord.length < 2)
+        return '';
     const workDir = cwd || process.cwd();
     try {
         const repo = await findRepoForCwd(workDir);
@@ -90,9 +93,7 @@ export async function augment(pattern, cwd) {
             await initLbug(repoId, repo.lbugPath);
         }
         // Step 1: BM25 search (fast, no embeddings)
-        const { results: bm25Results } = await searchFTSFromLbug(pattern, 10, repoId);
-        if (bm25Results.length === 0)
-            return '';
+        const { results: bm25Results, ftsAvailable } = await searchFTSFromLbug(pattern, 10, repoId);
         // Step 2: Map BM25 file results to symbols
         const symbolMatches = [];
         for (const result of bm25Results.slice(0, 5)) {
@@ -100,7 +101,7 @@ export async function augment(pattern, cwd) {
             try {
                 const symbols = await executeQuery(repoId, `
           MATCH (n) WHERE n.filePath = '${escaped}'
-          AND n.name CONTAINS '${pattern.replace(/'/g, "''").split(/\s+/)[0]}'
+          AND n.name CONTAINS '${patternFirstWord}'
           RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
           LIMIT 3
         `);
@@ -118,6 +119,25 @@ export async function augment(pattern, cwd) {
                 /* skip */
             }
         }
+        // When FTS indexes are unavailable (read-only DB, first run before indexes are built),
+        // fall back to a direct name CONTAINS query so enrichment still works.
+        if (symbolMatches.length === 0 && !ftsAvailable) {
+            const fallbackRows = await executeQuery(repoId, `
+        MATCH (n)
+        WHERE n.name CONTAINS '${patternFirstWord}'
+        RETURN n.id AS id, n.name AS name, labels(n)[0] AS type, n.filePath AS filePath
+        LIMIT 5
+      `).catch(() => []);
+            for (const sym of fallbackRows) {
+                symbolMatches.push({
+                    nodeId: sym.id || sym[0],
+                    name: sym.name || sym[1],
+                    type: sym.type || sym[2],
+                    filePath: sym.filePath || sym[3],
+                    score: 1.0,
+                });
+            }
+        }
         if (symbolMatches.length === 0)
             return '';
         // Step 3: Batch-fetch callers/callees/processes/cohesion for top matches

package/dist/core/embeddings/ast-utils.js

@@ -5,6 +5,7 @@
  */
 import { getLanguageFromFilename } from '../../_shared/index.js';
 import { createParserForLanguage, isLanguageAvailable, resolveLanguageKey, } from '../tree-sitter/parser-loader.js';
+import { parseSourceSafe } from '../tree-sitter/safe-parse.js';
 const parserCache = new Map();
 /**
  * Ensure parser is initialized and language is loaded, then parse content.
@@ -22,7 +23,7 @@ export const ensureAndParse = async (content, filePath) => {
         parserInstance = await createParserForLanguage(language, filePath);
         parserCache.set(parserKey, parserInstance);
     }
-    return parserInstance.parse(content);
+    return parseSourceSafe(parserInstance, content);
 };
 const FUNCTION_LIKE_TYPES = new Set([
     'function_declaration',