gitnexus 1.6.6-rc.98 → 1.6.6

package/dist/_shared/scope-resolution/registries/evidence.js.map

@@ -1 +1 @@
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package/dist/_shared/scope-resolution/registries/macro-registry.d.ts

@@ -0,0 +1,29 @@
+/**
+ * `MacroRegistry` — scope-aware lookup for macro definitions
+ * (`macro_rules!` in Rust; `#define` in C/C++) referenced from a macro
+ * invocation site.
+ *
+ * Thin wrapper over `lookupCore`, specialized for the macro namespace:
+ *
+ *   - `acceptedKinds` = `MACRO_KINDS` (`['Macro']` only). Crucially this
+ *     does NOT include `Function`/`Method`, so a `log!(…)` invocation can
+ *     never resolve to a same-named free function `fn log` — macros and
+ *     functions are disjoint namespaces (the false-`CALLS`-edge class the
+ *     #1934 review flagged).
+ *   - `useReceiverTypeBinding` is **false** — a macro invocation has no
+ *     receiver; resolution is name-through-the-lexical-chain + the global
+ *     qualified fallback, exactly like `ClassRegistry`.
+ *   - Arity is not applied — macros are variadic by nature.
+ */
+import type { Resolution, ScopeId } from '../types.js';
+import { type RegistryContext } from './context.js';
+export interface MacroRegistry {
+    /**
+     * Look up a macro definition by simple or scoped name anchored at
+     * `scope`. Returns a confidence-ranked `Resolution[]`; consume `[0]`
+     * for the best answer.
+     */
+    lookup(name: string, scope: ScopeId): readonly Resolution[];
+}
+export declare function buildMacroRegistry(ctx: RegistryContext): MacroRegistry;
+//# sourceMappingURL=macro-registry.d.ts.map

package/dist/_shared/scope-resolution/registries/macro-registry.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"macro-registry.d.ts","sourceRoot":"","sources":["../../../src/scope-resolution/registries/macro-registry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC;AAEvD,OAAO,EAAe,KAAK,eAAe,EAAE,MAAM,cAAc,CAAC;AAEjE,MAAM,WAAW,aAAa;IAC5B;;;;OAIG;IACH,MAAM,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,GAAG,SAAS,UAAU,EAAE,CAAC;CAC7D;AAED,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,eAAe,GAAG,aAAa,CAWtE"}

package/dist/_shared/scope-resolution/registries/macro-registry.js

@@ -0,0 +1,32 @@
+/**
+ * `MacroRegistry` — scope-aware lookup for macro definitions
+ * (`macro_rules!` in Rust; `#define` in C/C++) referenced from a macro
+ * invocation site.
+ *
+ * Thin wrapper over `lookupCore`, specialized for the macro namespace:
+ *
+ *   - `acceptedKinds` = `MACRO_KINDS` (`['Macro']` only). Crucially this
+ *     does NOT include `Function`/`Method`, so a `log!(…)` invocation can
+ *     never resolve to a same-named free function `fn log` — macros and
+ *     functions are disjoint namespaces (the false-`CALLS`-edge class the
+ *     #1934 review flagged).
+ *   - `useReceiverTypeBinding` is **false** — a macro invocation has no
+ *     receiver; resolution is name-through-the-lexical-chain + the global
+ *     qualified fallback, exactly like `ClassRegistry`.
+ *   - Arity is not applied — macros are variadic by nature.
+ */
+import { lookupCore } from './lookup-core.js';
+import { MACRO_KINDS } from './context.js';
+export function buildMacroRegistry(ctx) {
+    const params = {
+        acceptedKinds: MACRO_KINDS,
+        useReceiverTypeBinding: false,
+        ownerScopedContributor: null,
+    };
+    return {
+        lookup(name, scope) {
+            return lookupCore(name, scope, params, ctx);
+        },
+    };
+}
+//# sourceMappingURL=macro-registry.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"macro-registry.js","sourceRoot":"","sources":["../../../src/scope-resolution/registries/macro-registry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAGH,OAAO,EAAE,UAAU,EAAyB,MAAM,kBAAkB,CAAC;AACrE,OAAO,EAAE,WAAW,EAAwB,MAAM,cAAc,CAAC;AAWjE,MAAM,UAAU,kBAAkB,CAAC,GAAoB;IACrD,MAAM,MAAM,GAAqB;QAC/B,aAAa,EAAE,WAAW;QAC1B,sBAAsB,EAAE,KAAK;QAC7B,sBAAsB,EAAE,IAAI;KAC7B,CAAC;IACF,OAAO;QACL,MAAM,CAAC,IAAY,EAAE,KAAc;YACjC,OAAO,UAAU,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,CAAC,CAAC;QAC9C,CAAC;KACF,CAAC;AACJ,CAAC"}

package/dist/_shared/scope-resolution/symbol-definition.d.ts

@@ -56,5 +56,14 @@ export interface SymbolDefinition {
     isExplicit?: boolean;
     /** Links Method/Constructor/Property to owning Class/Struct/Trait nodeId */
     ownerId?: string;
+    /** #1982/#1993: bridge-held enclosing-namespace path (e.g. `NS1`, `Outer.Inner`)
+     *  tagged during the C++ resolution phase. Lets the graph bridge retry a
+     *  namespace-prefixed node-lookup key and lets the qualified-base resolver
+     *  break same-tail cross-namespace inheritance ties. A deliberate sidecar,
+     *  separate from `qualifiedName`: it does NOT participate in graph node
+     *  identity (node keys derive from filePath/type/qualifiedName) and leaves the
+     *  qualifiedName-keyed resolution index untouched. Absent for the common case
+     *  (non-namespace-nested defs and all non-C++ languages). */
+    namespacePrefix?: string;
 }
 //# sourceMappingURL=symbol-definition.d.ts.map

package/dist/_shared/scope-resolution/symbol-definition.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"symbol-definition.d.ts","sourceRoot":"","sources":["../../src/scope-resolution/symbol-definition.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAEnD,MAAM,WAAW,kBAAkB;IACjC,wFAAwF;IACxF,IAAI,EAAE,MAAM,CAAC;IACb,8EAA8E;IAC9E,EAAE,EAAE,MAAM,GAAG,OAAO,GAAG,UAAU,GAAG,gBAAgB,GAAG,SAAS,CAAC;IACjE,4CAA4C;IAC5C,WAAW,EAAE,OAAO,GAAG,YAAY,GAAG,YAAY,GAAG,SAAS,GAAG,SAAS,CAAC;IAC3E,4EAA4E;IAC5E,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,SAAS,CAAC;IAChB;;+FAE2F;IAC3F,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB;iHAC6G;IAC7G,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC;uFACmF;IACnF,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B;4FACwF;IACxF,oBAAoB,CAAC,EAAE,kBAAkB,EAAE,CAAC;IAC5C,6EAA6E;IAC7E,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,gGAAgG;IAChG,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,gGAAgG;IAChG,iBAAiB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC7B;;;;;yEAKqE;IACrE,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B;;4DAEwD;IACxD,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,4EAA4E;IAC5E,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB"}
+{"version":3,"file":"symbol-definition.d.ts","sourceRoot":"","sources":["../../src/scope-resolution/symbol-definition.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAEnD,MAAM,WAAW,kBAAkB;IACjC,wFAAwF;IACxF,IAAI,EAAE,MAAM,CAAC;IACb,8EAA8E;IAC9E,EAAE,EAAE,MAAM,GAAG,OAAO,GAAG,UAAU,GAAG,gBAAgB,GAAG,SAAS,CAAC;IACjE,4CAA4C;IAC5C,WAAW,EAAE,OAAO,GAAG,YAAY,GAAG,YAAY,GAAG,SAAS,GAAG,SAAS,CAAC;IAC3E,4EAA4E;IAC5E,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,SAAS,CAAC;IAChB;;+FAE2F;IAC3F,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB;iHAC6G;IAC7G,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC;uFACmF;IACnF,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B;4FACwF;IACxF,oBAAoB,CAAC,EAAE,kBAAkB,EAAE,CAAC;IAC5C,6EAA6E;IAC7E,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,gGAAgG;IAChG,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,gGAAgG;IAChG,iBAAiB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC7B;;;;;yEAKqE;IACrE,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B;;4DAEwD;IACxD,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,4EAA4E;IAC5E,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB;;;;;;;iEAO6D;IAC7D,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B"}

package/dist/_shared/scope-resolution/types.d.ts

@@ -363,7 +363,7 @@ export interface Reference {
     readonly toDef: DefId;
     /** Location of the reference in source. */
     readonly atRange: Range;
-    readonly kind: 'call' | 'read' | 'write' | 'type-reference' | 'inherits' | 'import-use';
+    readonly kind: 'call' | 'read' | 'write' | 'type-reference' | 'inherits' | 'import-use' | 'macro';
     readonly confidence: number;
     readonly evidence: readonly ResolutionEvidence[];
 }

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

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

@@ -18,11 +18,45 @@ export interface AIContextOptions {
     skipAgentsMd?: boolean;
     noStats?: boolean;
     skipSkills?: boolean;
+    /**
+     * Default branch used by the generated regression-compare example (#243).
+     * Resolved by the CLI (CLI flag > `.gitnexusrc` > auto-detect > "main"); a
+     * plain caller that omits it gets "main", preserving prior behavior.
+     */
+    defaultBranch?: string;
 }
+/**
+ * Strip backticks from a branch name before it is embedded in a Markdown
+ * inline-code span (#1996 tri-review P1). validateBranchName already rejects
+ * backticks for CLI/config/auto-detect inputs; this is the last-line defense at
+ * the generation sink so the embedding is provably safe regardless of caller.
+ */
+export declare function markdownSafeBranch(branch: string): string;
+export declare function generateGitNexusContent(projectName: string, stats: RepoStats, generatedSkills?: GeneratedSkillInfo[], groupNames?: string[], noStats?: boolean, skipSkills?: boolean, runnerPath?: string, defaultBranch?: string): string;
 /**
  * Generate AI context files after indexing
  */
-export declare function generateAIContextFiles(repoPath: string, _storagePath: string, projectName: string, stats: RepoStats, generatedSkills?: GeneratedSkillInfo[], options?: AIContextOptions): Promise<{
+export declare function generateAIContextFiles(repoPath: string, storagePath: string, projectName: string, stats: RepoStats, generatedSkills?: GeneratedSkillInfo[], options?: AIContextOptions): Promise<{
+    files: string[];
+}>;
+/**
+ * Refresh only the `base_ref: "..."` value inside the GitNexus block of an
+ * already-generated AGENTS.md / CLAUDE.md, in place (#1996 tri-review P2).
+ *
+ * The `alreadyUpToDate` analyze fast path returns before the normal
+ * {@link generateAIContextFiles} call, so a changed `.gitnexusrc` defaultBranch
+ * (or `--default-branch`) would otherwise not take effect until the next
+ * re-index. This does a surgical line update that preserves the rest of the
+ * block — including community-skill rows written by a prior `--skills` run —
+ * rather than regenerating (which would drop those rows on a no-`--skills` run).
+ *
+ * Best-effort: missing files, a missing/blank block, or a block with no
+ * `base_ref` line (e.g. a user-trimmed keep block) are silently skipped. Writes
+ * only when the value actually changes, so a routine up-to-date run is a no-op.
+ */
+export declare function refreshBaseRefLine(repoPath: string, defaultBranch: string, options?: {
+    skipAgentsMd?: boolean;
+}): Promise<{
     files: string[];
 }>;
 export {};

package/dist/cli/ai-context.js

@@ -68,7 +68,28 @@ async function findGroupsContainingRegistryName(registryName) {
     }
     return hits;
 }
-function generateGitNexusContent(projectName, stats, generatedSkills, groupNames, noStats, skipSkills) {
+/**
+ * Strip backticks from a branch name before it is embedded in a Markdown
+ * inline-code span (#1996 tri-review P1). validateBranchName already rejects
+ * backticks for CLI/config/auto-detect inputs; this is the last-line defense at
+ * the generation sink so the embedding is provably safe regardless of caller.
+ */
+export function markdownSafeBranch(branch) {
+    return branch.replace(/`/g, '');
+}
+export function generateGitNexusContent(projectName, stats, generatedSkills, groupNames, noStats, skipSkills, 
+// Project-relative path to the runner `gitnexus analyze` drops next to the
+// index (#1945). Referenced by docs so a single CLI-neutral command resolves
+// the available runner (global `gitnexus` → `pnpm dlx` → `npx`) at call time.
+runnerPath = '.gitnexus/run.cjs', 
+// Default branch for the regression-compare example (#243). Configurable so
+// projects on `develop`/`master`/etc. don't get `base_ref: "main"` rewritten
+// back over their fix on every analyze. The value is embedded inside a
+// Markdown inline-code span: validateBranchName rejects backticks upstream,
+// and `markdownSafeBranch` strips any remaining backtick here as defense in
+// depth, so JSON.stringify's quote/escape handling is sufficient and the
+// branch cannot break out of the span (#1996 tri-review P1).
+defaultBranch = 'main') {
     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\` |`)
@@ -93,27 +114,35 @@ function generateGitNexusContent(projectName, stats, generatedSkills, groupNames
 |------|---------------------|
 ${tableBody}`
         : '';
+    // Docs reference the project-local runner `gitnexus analyze` writes (#1945):
+    // a single, CLI-neutral, machine-independent command (no per-machine churn,
+    // #1706) that auto-selects the available runner at call time. Kept terse to
+    // stay under the CLAUDE.md block token budget (#856); the cli skill carries the
+    // full bootstrap + npm-11 fallback (`node.target is null` npx install crash).
+    const runner = `node ${runnerPath}`;
+    const bootstrapNote = `No \`${runnerPath}\` yet? \`npx gitnexus analyze\` ` +
+        '(npm 11 crash → `npm i -g gitnexus`; #1939).';
     return `${GITNEXUS_START_MARKER}
 # GitNexus — Code Intelligence
 
 This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${stats.nodes || 0} symbols, ${stats.edges || 0} relationships, ${stats.processes || 0} execution flows)`}. Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
 
-> If any GitNexus tool warns the index is stale, run \`npx gitnexus analyze\` in terminal first.
+> Index stale? Run \`${runner} analyze\` from the project root — it auto-selects an available runner. ${bootstrapNote}
 
 ## Always Do
 
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run \`gitnexus_impact({target: "symbolName", direction: "upstream"})\` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run \`gitnexus_detect_changes()\` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run \`impact({target: "symbolName", direction: "upstream"})\` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run \`detect_changes()\` before committing** to verify your changes only affect expected symbols and execution flows. For regression review, compare against the default branch: \`detect_changes({scope: "compare", base_ref: ${JSON.stringify(markdownSafeBranch(defaultBranch))}})\`.
 - **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use \`gitnexus_query({query: "concept"})\` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use \`gitnexus_context({name: "symbolName"})\`.
+- When exploring unfamiliar code, use \`query({query: "concept"})\` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use \`context({name: "symbolName"})\`.
 
 ## Never Do
 
-- NEVER edit a function, class, or method without first running \`gitnexus_impact\` on it.
+- NEVER edit a function, class, or method without first running \`impact\` on it.
 - NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
-- NEVER rename symbols with find-and-replace — use \`gitnexus_rename\` which understands the call graph.
-- NEVER commit changes without running \`gitnexus_detect_changes()\` to check affected scope.
+- NEVER rename symbols with find-and-replace — use \`rename\` which understands the call graph.
+- NEVER commit changes without running \`detect_changes()\` to check affected scope.
 
 ## Resources
 
@@ -127,7 +156,7 @@ This project is indexed by GitNexus as **${projectName}**${noStats ? '' : ` (${s
 ${groupNames && groupNames.length > 0
         ? `## Cross-Repo Groups
 
-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>\`.
+This repository is listed under GitNexus **group(s): ${groupNames.join(', ')}** (see \`~/.gitnexus/groups/\`). For cross-repo analysis, use MCP tools \`impact\`, \`query\`, and \`context\` with \`repo\` set to \`@<groupName>\` or \`@<groupName>/<memberPath>\` (paths match keys in that group’s \`group.yaml\`). Use \`group_list\` / \`group_sync\` for membership and sync. From the project root: \`${runner} group list\`, \`${runner} group sync <name>\`, \`${runner} group impact <name> --target <symbol> --repo <group-path>\` (the \`${runnerPath}\` path is repo-root-relative).
 
 `
         : ''}${skillsTable
@@ -302,9 +331,24 @@ Use GitNexus tools to accomplish this task.
 /**
  * Generate AI context files after indexing
  */
-export async function generateAIContextFiles(repoPath, _storagePath, projectName, stats, generatedSkills, options) {
+export async function generateAIContextFiles(repoPath, storagePath, projectName, stats, generatedSkills, options) {
     const groupNames = await findGroupsContainingRegistryName(projectName);
-    const content = generateGitNexusContent(projectName, stats, generatedSkills, groupNames, options?.noStats, options?.skipSkills);
+    // Drop a project-local runner next to the index (#1945) so the generated docs
+    // can reference one CLI-neutral command that resolves the available runner at
+    // call time. It is a copy of the canonical self-contained resolver, which the
+    // CLI and hooks already share; failure to copy is non-fatal (docs carry a
+    // bootstrap fallback). `runnerPath` is project-relative with POSIX separators
+    // so the emitted command is identical across platforms.
+    const runnerPath = path.relative(repoPath, path.join(storagePath, 'run.cjs')).replace(/\\/g, '/');
+    try {
+        const runnerSrc = path.join(__dirname, '..', '..', 'hooks', 'claude', 'resolve-analyze-cmd.cjs');
+        await fs.mkdir(storagePath, { recursive: true });
+        await fs.copyFile(runnerSrc, path.join(storagePath, 'run.cjs'));
+    }
+    catch (err) {
+        logger.warn(`Could not write GitNexus runner to ${runnerPath}: ${String(err)}`);
+    }
+    const content = generateGitNexusContent(projectName, stats, generatedSkills, groupNames, options?.noStats, options?.skipSkills, runnerPath, options?.defaultBranch ?? 'main');
     const createdFiles = [];
     if (!options?.skipAgentsMd) {
         // Create AGENTS.md (standard for Cursor, Windsurf, OpenCode, Cline, etc.)
@@ -332,3 +376,58 @@ export async function generateAIContextFiles(repoPath, _storagePath, projectName
     }
     return { files: createdFiles };
 }
+/**
+ * Refresh only the `base_ref: "..."` value inside the GitNexus block of an
+ * already-generated AGENTS.md / CLAUDE.md, in place (#1996 tri-review P2).
+ *
+ * The `alreadyUpToDate` analyze fast path returns before the normal
+ * {@link generateAIContextFiles} call, so a changed `.gitnexusrc` defaultBranch
+ * (or `--default-branch`) would otherwise not take effect until the next
+ * re-index. This does a surgical line update that preserves the rest of the
+ * block — including community-skill rows written by a prior `--skills` run —
+ * rather than regenerating (which would drop those rows on a no-`--skills` run).
+ *
+ * Best-effort: missing files, a missing/blank block, or a block with no
+ * `base_ref` line (e.g. a user-trimmed keep block) are silently skipped. Writes
+ * only when the value actually changes, so a routine up-to-date run is a no-op.
+ */
+export async function refreshBaseRefLine(repoPath, defaultBranch, options) {
+    if (options?.skipAgentsMd)
+        return { files: [] };
+    const replacement = `base_ref: ${JSON.stringify(markdownSafeBranch(defaultBranch))}`;
+    const updated = [];
+    for (const name of ['AGENTS.md', 'CLAUDE.md']) {
+        const filePath = path.join(repoPath, name);
+        if (!(await fileExists(filePath)))
+            continue;
+        let content;
+        try {
+            content = await fs.readFile(filePath, 'utf-8');
+        }
+        catch {
+            continue;
+        }
+        const startIdx = findSectionMarkerIndex(content, GITNEXUS_START_MARKER);
+        if (startIdx === -1)
+            continue;
+        const endIdx = findSectionMarkerIndex(content, GITNEXUS_END_MARKER, startIdx);
+        if (endIdx === -1 || endIdx <= startIdx)
+            continue;
+        const blockEnd = endIdx + GITNEXUS_END_MARKER.length;
+        const block = content.substring(startIdx, blockEnd);
+        // Only the generated regression example carries a base_ref line, and only
+        // one per block; replace its quoted value while leaving the rest untouched.
+        const newBlock = block.replace(/base_ref: "(?:[^"\\]|\\.)*"/, replacement);
+        if (newBlock === block)
+            continue; // no base_ref line present, or already current
+        const newContent = content.substring(0, startIdx) + newBlock + content.substring(blockEnd);
+        try {
+            await fs.writeFile(filePath, newContent, 'utf-8');
+            updated.push(name);
+        }
+        catch {
+            // best-effort — never fail analyze over a context refresh
+        }
+    }
+    return { files: updated };
+}

package/dist/cli/analyze-config.d.ts

@@ -0,0 +1,92 @@
+/**
+ * Project-local `.gitnexusrc` support for `gitnexus analyze` (#243).
+ *
+ * Lets a repository commit recurring `analyze` defaults — default branch for the
+ * generated regression example, AI-context / skills opt-outs, embedding knobs —
+ * so contributors don't re-pass the same flags on every run. Design rules:
+ *
+ *   - Config is repo-local (`.gitnexusrc` at the resolved repo root). It is NOT
+ *     read from `.gitnexus/` because that directory is index storage and is
+ *     commonly gitignored.
+ *   - JSON only. No YAML, no `package.json` field, no global `~/.gitnexus` file
+ *     in this pass.
+ *   - CLI flags always override config (see {@link mergeAnalyzeOptions}).
+ *   - Fail closed: unknown keys, wrong value types, conflicting aliases, and
+ *     invalid JSON all throw {@link GitNexusRcError} so a typo never silently
+ *     no-ops. Errors are actionable and surface before any expensive analysis.
+ *   - Config values never reach a shell. Strings are validated against control
+ *     and hidden/bidirectional characters so they cannot inject markdown,
+ *     JSON, or hidden controls into generated context files.
+ *
+ * Both a flat shape and a nested `analyze` block are accepted:
+ *
+ *     { "defaultBranch": "develop", "skipContextFiles": true }
+ *     { "analyze": { "defaultBranch": "develop", "skipSkills": true } }
+ *
+ * When both set the same option, the nested `analyze` block wins (deterministic,
+ * documented precedence). Conflicting *aliases at the same level* (e.g. both
+ * `defaultBranch` and `branch`) are rejected.
+ */
+import type { AnalyzeOptions } from './analyze.js';
+export declare const GITNEXUS_RC_FILENAME = ".gitnexusrc";
+/** Final fallback when no branch is configured or detectable. */
+export declare const DEFAULT_BRANCH_FALLBACK = "main";
+/**
+ * Thrown for any `.gitnexusrc` problem (missing-file is NOT an error — it
+ * returns `undefined`). The message is user-facing and names the file so the
+ * CLI can print it verbatim before starting the progress bar.
+ */
+export declare class GitNexusRcError extends Error {
+    constructor(message: string);
+}
+/**
+ * Validate a user-supplied branch name (from CLI or `.gitnexusrc`). Returns the
+ * trimmed name or throws {@link GitNexusRcError}. Conservative but accepts the
+ * shapes real branches use (`feature/foo-bar`, `release/1.2`, `develop`).
+ */
+export declare function validateBranchName(value: string, source: string): string;
+/**
+ * Best-effort validation for an auto-detected branch (from git). Never throws —
+ * returns `undefined` for anything unusable so the resolver falls back to the
+ * next precedence tier.
+ */
+export declare function sanitizeDetectedBranch(value: string | null | undefined): string | undefined;
+/**
+ * Locate, read, parse, validate, and normalize `.gitnexusrc` at `repoRoot`.
+ *
+ * @returns the normalized config defaults, or `undefined` when no file exists
+ *          (the normal case). Throws {@link GitNexusRcError} on any problem.
+ */
+export declare function loadAnalyzeConfig(repoRoot: string): Partial<AnalyzeOptions> | undefined;
+/**
+ * Merge CLI options over `.gitnexusrc` defaults. CLI wins whenever it provides a
+ * value — including an explicit `false` (so an explicit CLI off-switch beats a
+ * config `true`). Config fills only the genuinely-unset (`undefined`) options.
+ *
+ * `stats` is special: Commander always materializes it (`true` by default,
+ * `false` only when `--no-stats` is passed), so plain `??` can't tell "default
+ * on" from "explicitly on". The rule is: a passed `--no-stats` (`stats: false`)
+ * always wins; otherwise the config value applies. There is intentionally no
+ * `--stats` counter-flag, so config can only turn stats off, not force it back
+ * on against a `--no-stats`.
+ *
+ * `defaultBranch` is NOT resolved here — see {@link resolveDefaultBranch}, which
+ * applies the CLI > config > auto-detect > "main" precedence chain.
+ */
+export declare function mergeAnalyzeOptions(cli: AnalyzeOptions, config: Partial<AnalyzeOptions> | undefined): AnalyzeOptions;
+/**
+ * Resolve the default branch threaded into generated context, applying the
+ * precedence chain:
+ *
+ *   CLI `--default-branch` > `.gitnexusrc` `defaultBranch`/`branch`
+ *     > auto-detected `origin/HEAD` > {@link DEFAULT_BRANCH_FALLBACK} ("main").
+ *
+ * User-supplied values (CLI, config) are validated strictly and throw on bad
+ * input. The auto-detected value is best-effort and silently ignored if
+ * unusable.
+ */
+export declare function resolveDefaultBranch(input: {
+    cliBranch?: string;
+    configBranch?: string;
+    detectedBranch?: string | null;
+}): string;