gitnexus 1.6.8-rc.2 → 1.6.8-rc.21

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

@@ -11,6 +11,9 @@ export declare const cliResources: {
         readonly 'list.title': "Indexed Repositories ({{count}})";
         readonly 'list.indexed': "Indexed";
         readonly 'list.commit': "Commit";
+        readonly 'list.branch': "Branch";
+        readonly 'list.branchIndexes': "Branch indexes";
+        readonly 'list.branchLine': "{{branch}} ({{commit}}, {{indexed}})";
         readonly 'list.stats': "Stats";
         readonly 'list.statsValue': "{{files}} files, {{symbols}} symbols, {{edges}} edges";
         readonly 'list.clusters': "Clusters";
@@ -24,6 +27,9 @@ export declare const cliResources: {
         readonly 'status.indexed': "Indexed";
         readonly 'status.indexedCommit': "Indexed commit";
         readonly 'status.currentCommit': "Current commit";
+        readonly 'status.branch': "Branch";
+        readonly 'status.detached': "(detached HEAD)";
+        readonly 'status.branchNotIndexed': "⚠️ current branch not indexed (primary index is for '{{primary}}'; run gitnexus analyze)";
         readonly 'status.status': "Status";
         readonly 'status.upToDate': "✅ up-to-date";
         readonly 'status.stale': "⚠️ stale (re-run gitnexus analyze)";
@@ -31,6 +37,9 @@ export declare const cliResources: {
         readonly 'clean.deletedRepo': "Deleted: {{name}} ({{storagePath}})";
         readonly 'clean.notFoundHere': "No indexed repository found in this directory.";
         readonly 'clean.deleteCurrent': "This will delete the GitNexus index for: {{repoName}}";
+        readonly 'clean.branchNotIndexed': "No indexed branch named \"{{branch}}\" for this repository.";
+        readonly 'clean.deleteBranch': "This will delete the branch index \"{{branch}}\" at: {{path}}";
+        readonly 'clean.deletedBranch': "Deleted branch index: {{branch}}";
         readonly 'clean.lbugSidecars.state': "LadybugDB sidecar state: {{state}}";
         readonly 'clean.lbugSidecars.none': "No quarantined LadybugDB missing-shadow WAL sidecars found.";
         readonly 'clean.lbugSidecars.preview': "This will delete {{count}} quarantined LadybugDB missing-shadow WAL sidecar(s):";
@@ -118,6 +127,7 @@ export declare const cliResources: {
         readonly 'help.command.impact.description': "Blast radius analysis: what breaks if you change a symbol";
         readonly 'help.command.cypher.description': "Execute raw Cypher query against the knowledge graph";
         readonly 'help.command.detectChanges.description': "Map git diff hunks to indexed symbols and affected execution flows";
+        readonly 'help.command.check.description': "Run structural checks against the indexed graph";
         readonly 'help.command.evalServer.description': "Start lightweight HTTP server for fast tool calls during evaluation";
         readonly 'help.command.group.description': "Manage repository groups for cross-index impact analysis";
         readonly 'help.command.group.create.description': "Create a new group with template group.yaml";
@@ -157,6 +167,7 @@ export declare const cliResources: {
         readonly 'help.option.force.confirmation': "Skip confirmation prompt";
         readonly 'help.option.uninstall.force': "Apply the changes (default is a dry-run preview)";
         readonly 'help.option.clean.all': "Clean all indexed repos";
+        readonly 'help.option.clean.branch': "Delete only the named branch index (not the primary)";
         readonly 'help.option.clean.lbugSidecars': "Clean quarantined LadybugDB missing-shadow WAL sidecars";
         readonly 'help.option.wiki.force': "Force full regeneration even if up to date";
         readonly 'help.option.wiki.provider': "LLM provider: openai, openrouter, azure, custom, cursor, claude, codex, or opencode (default: openai)";
@@ -179,6 +190,7 @@ export declare const cliResources: {
         readonly 'help.option.query.limit': "Max processes to return (default: 5)";
         readonly 'help.option.content': "Include full symbol source code";
         readonly 'help.option.repo.target': "Target repository";
+        readonly 'help.option.branch': "Scope to a specific branch index (multi-branch repos)";
         readonly 'help.option.context.uid': "Direct symbol UID (zero-ambiguity lookup)";
         readonly 'help.option.context.file': "File path to disambiguate common names";
         readonly 'help.option.impact.kind': "Kind filter to disambiguate common names (e.g. Function, Class, Method)";
@@ -190,6 +202,7 @@ export declare const cliResources: {
         readonly 'help.option.impact.summaryOnly': "Return counts and risk only, omit symbol list";
         readonly 'help.option.detectChanges.scope': "What to analyze: unstaged, staged, all, or compare";
         readonly 'help.option.detectChanges.baseRef': "Branch/commit for compare scope (e.g. main)";
+        readonly 'help.option.check.cycles': "Detect circular imports and fail when any are found";
         readonly 'help.option.evalServer.host': "Bind address (default: 127.0.0.1, use 0.0.0.0 to expose to all interfaces)";
         readonly 'help.option.evalServer.idleTimeout': "Auto-shutdown after N seconds idle (0 = disabled)";
         readonly 'help.option.group.create.force': "Overwrite existing group";
@@ -224,6 +237,9 @@ export declare const cliResources: {
         'list.title': string;
         'list.indexed': string;
         'list.commit': string;
+        'list.branch': string;
+        'list.branchIndexes': string;
+        'list.branchLine': string;
         'list.stats': string;
         'list.statsValue': string;
         'list.clusters': string;
@@ -237,6 +253,9 @@ export declare const cliResources: {
         'status.indexed': string;
         'status.indexedCommit': string;
         'status.currentCommit': string;
+        'status.branch': string;
+        'status.detached': string;
+        'status.branchNotIndexed': string;
         'status.status': string;
         'status.upToDate': string;
         'status.stale': string;
@@ -244,6 +263,9 @@ export declare const cliResources: {
         'clean.deletedRepo': string;
         'clean.notFoundHere': string;
         'clean.deleteCurrent': string;
+        'clean.branchNotIndexed': string;
+        'clean.deleteBranch': string;
+        'clean.deletedBranch': string;
         'clean.lbugSidecars.state': string;
         'clean.lbugSidecars.none': string;
         'clean.lbugSidecars.preview': string;
@@ -331,6 +353,7 @@ export declare const cliResources: {
         'help.command.impact.description': string;
         'help.command.cypher.description': string;
         'help.command.detectChanges.description': string;
+        'help.command.check.description': string;
         'help.command.evalServer.description': string;
         'help.command.group.description': string;
         'help.command.group.create.description': string;
@@ -370,6 +393,7 @@ export declare const cliResources: {
         'help.option.force.confirmation': string;
         'help.option.uninstall.force': string;
         'help.option.clean.all': string;
+        'help.option.clean.branch': string;
         'help.option.clean.lbugSidecars': string;
         'help.option.wiki.force': string;
         'help.option.wiki.provider': string;
@@ -392,6 +416,7 @@ export declare const cliResources: {
         'help.option.query.limit': string;
         'help.option.content': string;
         'help.option.repo.target': string;
+        'help.option.branch': string;
         'help.option.context.uid': string;
         'help.option.context.file': string;
         'help.option.impact.kind': string;
@@ -403,6 +428,7 @@ export declare const cliResources: {
         'help.option.impact.summaryOnly': string;
         'help.option.detectChanges.scope': string;
         'help.option.detectChanges.baseRef': string;
+        'help.option.check.cycles': string;
         'help.option.evalServer.host': string;
         'help.option.evalServer.idleTimeout': string;
         'help.option.group.create.force': string;

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

@@ -10,6 +10,9 @@ export declare const zhCN: {
     'list.title': string;
     'list.indexed': string;
     'list.commit': string;
+    'list.branch': string;
+    'list.branchIndexes': string;
+    'list.branchLine': string;
     'list.stats': string;
     'list.statsValue': string;
     'list.clusters': string;
@@ -23,6 +26,9 @@ export declare const zhCN: {
     'status.indexed': string;
     'status.indexedCommit': string;
     'status.currentCommit': string;
+    'status.branch': string;
+    'status.detached': string;
+    'status.branchNotIndexed': string;
     'status.status': string;
     'status.upToDate': string;
     'status.stale': string;
@@ -30,6 +36,9 @@ export declare const zhCN: {
     'clean.deletedRepo': string;
     'clean.notFoundHere': string;
     'clean.deleteCurrent': string;
+    'clean.branchNotIndexed': string;
+    'clean.deleteBranch': string;
+    'clean.deletedBranch': string;
     'clean.lbugSidecars.state': string;
     'clean.lbugSidecars.none': string;
     'clean.lbugSidecars.preview': string;
@@ -117,6 +126,7 @@ export declare const zhCN: {
     'help.command.impact.description': string;
     'help.command.cypher.description': string;
     'help.command.detectChanges.description': string;
+    'help.command.check.description': string;
     'help.command.evalServer.description': string;
     'help.command.group.description': string;
     'help.command.group.create.description': string;
@@ -156,6 +166,7 @@ export declare const zhCN: {
     'help.option.force.confirmation': string;
     'help.option.uninstall.force': string;
     'help.option.clean.all': string;
+    'help.option.clean.branch': string;
     'help.option.clean.lbugSidecars': string;
     'help.option.wiki.force': string;
     'help.option.wiki.provider': string;
@@ -178,6 +189,7 @@ export declare const zhCN: {
     'help.option.query.limit': string;
     'help.option.content': string;
     'help.option.repo.target': string;
+    'help.option.branch': string;
     'help.option.context.uid': string;
     'help.option.context.file': string;
     'help.option.impact.kind': string;
@@ -189,6 +201,7 @@ export declare const zhCN: {
     'help.option.impact.summaryOnly': string;
     'help.option.detectChanges.scope': string;
     'help.option.detectChanges.baseRef': string;
+    'help.option.check.cycles': string;
     'help.option.evalServer.host': string;
     'help.option.evalServer.idleTimeout': string;
     'help.option.group.create.force': string;

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

@@ -10,6 +10,9 @@ export const zhCN = {
     'list.title': '已索引仓库（{{count}}）',
     'list.indexed': '索引时间',
     'list.commit': '提交',
+    'list.branch': '分支',
+    'list.branchIndexes': '分支索引',
+    'list.branchLine': '{{branch}}（{{commit}}，{{indexed}}）',
     'list.stats': '统计',
     'list.statsValue': '{{files}} 个文件，{{symbols}} 个符号，{{edges}} 条边',
     'list.clusters': '聚类',
@@ -23,6 +26,9 @@ export const zhCN = {
     'status.indexed': '索引时间',
     'status.indexedCommit': '索引提交',
     'status.currentCommit': '当前提交',
+    'status.branch': '分支',
+    'status.detached': '（分离 HEAD）',
+    'status.branchNotIndexed': "⚠️ 当前分支未索引（主索引对应 '{{primary}}'；请运行 gitnexus analyze）",
     'status.status': '状态',
     'status.upToDate': '✅ 已是最新',
     'status.stale': '⚠️ 已过期（重新运行 gitnexus analyze）',
@@ -30,6 +36,9 @@ export const zhCN = {
     'clean.deletedRepo': '已删除：{{name}}（{{storagePath}}）',
     'clean.notFoundHere': '当前目录未找到已索引仓库。',
     'clean.deleteCurrent': '将删除该仓库的 GitNexus 索引：{{repoName}}',
+    'clean.branchNotIndexed': '该仓库没有名为 “{{branch}}” 的已索引分支。',
+    'clean.deleteBranch': '将删除分支索引 “{{branch}}”，路径：{{path}}',
+    'clean.deletedBranch': '已删除分支索引：{{branch}}',
     'clean.lbugSidecars.state': 'LadybugDB sidecar 状态：{{state}}',
     'clean.lbugSidecars.none': '未找到已隔离的 LadybugDB missing-shadow WAL sidecar。',
     'clean.lbugSidecars.preview': '将删除 {{count}} 个已隔离的 LadybugDB missing-shadow WAL sidecar：',
@@ -117,6 +126,7 @@ export const zhCN = {
     'help.command.impact.description': '影响面分析：修改符号会影响什么',
     'help.command.cypher.description': '对知识图谱执行原始 Cypher 查询',
     'help.command.detectChanges.description': '将 git diff hunk 映射到已索引符号和受影响执行流程',
+    'help.command.check.description': '对已索引图谱运行结构检查',
     'help.command.evalServer.description': '启动轻量 HTTP 服务器，用于评测期间的快速工具调用',
     'help.command.group.description': '管理仓库组，用于跨索引影响分析',
     'help.command.group.create.description': '使用模板 group.yaml 创建新仓库组',
@@ -156,6 +166,7 @@ export const zhCN = {
     'help.option.force.confirmation': '跳过确认提示',
     'help.option.uninstall.force': '应用更改（默认仅为预演预览）',
     'help.option.clean.all': '清理所有已索引仓库',
+    'help.option.clean.branch': '仅删除指定分支的索引（不影响主索引）',
     'help.option.clean.lbugSidecars': '清理已隔离的 LadybugDB missing-shadow WAL sidecar',
     'help.option.wiki.force': '即使已是最新也强制完整重新生成',
     'help.option.wiki.provider': 'LLM 提供商：openai、openrouter、azure、custom、cursor、claude、codex 或 opencode（默认：openai）',
@@ -178,6 +189,7 @@ export const zhCN = {
     'help.option.query.limit': '最多返回的流程数（默认：5）',
     'help.option.content': '包含完整符号源码',
     'help.option.repo.target': '目标仓库',
+    'help.option.branch': '将查询限定到指定分支的索引（多分支仓库）',
     'help.option.context.uid': '直接符号 UID（零歧义查找）',
     'help.option.context.file': '用于消除常见名称歧义的文件路径',
     'help.option.impact.kind': '用于消除常见名称歧义的类型过滤（如 Function、Class、Method）',
@@ -189,6 +201,7 @@ export const zhCN = {
     'help.option.impact.summaryOnly': '仅返回计数和风险等级，省略符号列表',
     'help.option.detectChanges.scope': '分析范围：unstaged、staged、all 或 compare',
     'help.option.detectChanges.baseRef': 'compare 范围的分支/提交（例如 main）',
+    'help.option.check.cycles': '检测循环导入，并在发现循环时失败',
     'help.option.evalServer.host': '绑定地址（默认：127.0.0.1；用 0.0.0.0 暴露到所有网卡）',
     'help.option.evalServer.idleTimeout': '空闲 N 秒后自动关闭（0 = 禁用）',
     'help.option.group.create.force': '覆盖现有仓库组',

package/dist/cli/index.js

@@ -32,8 +32,13 @@ program
     .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('--pdg', 'Build the control-flow-graph / PDG substrate (BasicBlock nodes + CFG edges) ' +
+    'for supported languages. Opt-in; off by default. (#2081 M1)')
     .option('--default-branch <branch>', 'Default branch used in the generated regression-compare example (base_ref). ' +
     'Falls back to .gitnexusrc, then auto-detected origin/HEAD, then "main".')
+    .option('--branch <name>', 'Index the working tree under a specific branch slot (multi-branch indexing). ' +
+    'Defaults to the checked-out branch; the primary/first-indexed branch keeps the ' +
+    'flat index and others get their own. Distinct from --default-branch (cosmetic base_ref).')
     .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/). ' +
@@ -89,6 +94,7 @@ program
     .description('Delete GitNexus index for current repo')
     .option('-f, --force', 'Skip confirmation prompt')
     .option('--all', 'Clean all indexed repos')
+    .option('--branch <name>', 'Delete only the named branch index (not the primary)')
     .option('--lbug-sidecars', 'Clean quarantined LadybugDB missing-shadow WAL sidecars')
     .action(createLazyAction(() => import('./clean.js'), 'cleanCommand'));
 program
@@ -135,6 +141,7 @@ program
     .command('query <search_query>')
     .description('Search the knowledge graph for execution flows related to a concept')
     .option('-r, --repo <name>', 'Target repository (omit if only one indexed)')
+    .option('--branch <name>', 'Scope to a specific branch index (multi-branch repos)')
     .option('-c, --context <text>', 'Task context to improve ranking')
     .option('-g, --goal <text>', 'What you want to find')
     .option('-l, --limit <n>', 'Max processes to return (default: 5)')
@@ -144,6 +151,7 @@ program
     .command('context [name]')
     .description('360-degree view of a code symbol: callers, callees, processes')
     .option('-r, --repo <name>', 'Target repository')
+    .option('--branch <name>', 'Scope to a specific branch index (multi-branch repos)')
     .option('-u, --uid <uid>', 'Direct symbol UID (zero-ambiguity lookup)')
     .option('-f, --file <path>', 'File path to disambiguate common names')
     .option('--content', 'Include full symbol source code')
@@ -153,6 +161,7 @@ program
     .description('Blast radius analysis: what breaks if you change a symbol')
     .option('-d, --direction <dir>', 'upstream (dependants) or downstream (dependencies)', 'upstream')
     .option('-r, --repo <name>', 'Target repository')
+    .option('--branch <name>', 'Scope to a specific branch index (multi-branch repos)')
     .option('-u, --uid <uid>', 'Direct symbol UID (zero-ambiguity lookup)')
     .option('-f, --file <path>', 'File path to disambiguate common names')
     .option('--kind <kind>', 'Kind filter to disambiguate common names (e.g. Function, Class, Method)')
@@ -166,6 +175,7 @@ program
     .command('cypher <query>')
     .description('Execute raw Cypher query against the knowledge graph')
     .option('-r, --repo <name>', 'Target repository')
+    .option('--branch <name>', 'Scope to a specific branch index (multi-branch repos)')
     .action(createLbugLazyAction(() => import('./tool.js'), 'cypherCommand'));
 program
     .command('detect-changes')
@@ -174,7 +184,16 @@ program
     .option('-s, --scope <scope>', 'What to analyze: unstaged, staged, all, or compare', 'unstaged')
     .option('-b, --base-ref <ref>', 'Branch/commit for compare scope (e.g. main)')
     .option('-r, --repo <name>', 'Target repository')
+    .option('--branch <name>', 'Scope to a specific branch index (multi-branch repos)')
     .action(createLbugLazyAction(() => import('./tool.js'), 'detectChangesCommand'));
+program
+    .command('check')
+    .description('Run structural checks against the indexed graph')
+    .option('--cycles', 'Detect circular imports and fail when any are found')
+    .option('--json', 'Emit machine-readable JSON')
+    .option('-r, --repo <name>', 'Target repository')
+    .option('--branch <name>', 'Scope to a specific branch index (multi-branch repos)')
+    .action(createLbugLazyAction(() => import('./tool.js'), 'checkCommand'));
 // ─── Eval Server (persistent daemon for SWE-bench) ─────────────────
 program
     .command('eval-server')

package/dist/cli/list.js

@@ -31,6 +31,8 @@ export const listCommand = async () => {
         console.log(`    ${t('common.path')}:    ${entry.path}`);
         console.log(`    ${t('list.indexed')}: ${indexedDate}`);
         console.log(`    ${t('list.commit')}:  ${commitShort}`);
+        if (entry.branch)
+            console.log(`    ${t('list.branch')}:  ${entry.branch}`);
         console.log(`    ${t('list.stats')}:   ${t('list.statsValue', {
             files: stats.files ?? 0,
             symbols: stats.nodes ?? 0,
@@ -40,6 +42,16 @@ export const listCommand = async () => {
             console.log(`    ${t('list.clusters')}:   ${stats.communities}`);
         if (stats.processes)
             console.log(`    ${t('list.processes')}:  ${stats.processes}`);
+        // Per-branch indexes (#2106). Only rendered when extra branches were
+        // indexed for this path, so single-branch output is unchanged.
+        if (entry.branches && entry.branches.length > 0) {
+            console.log(`    ${t('list.branchIndexes')}:`);
+            for (const b of entry.branches) {
+                const bCommit = b.lastCommit?.slice(0, 7) || t('list.unknown');
+                const bIndexed = new Date(b.indexedAt).toLocaleString();
+                console.log(`      ${t('list.branchLine', { branch: b.branch, commit: bCommit, indexed: bIndexed })}`);
+            }
+        }
         console.log('');
     }
 };

package/dist/cli/optional-grammars.d.ts

@@ -1,15 +1,13 @@
 /**
  * Optional grammar availability check.
  *
- * tree-sitter-dart, tree-sitter-proto, and tree-sitter-swift are vendored
- * under vendor/ and materialized into node_modules/ at postinstall. Dart
- * and Proto are built from source with node-gyp; Swift ships platform
- * prebuilds activated via node-gyp-build. tree-sitter-kotlin is a declared
- * optionalDependency (not vendored). All can be skipped via
+ * tree-sitter-dart, -proto, -swift, and -kotlin are vendored under vendor/ and
+ * loaded from there by absolute path (NEVER copied into node_modules — see
+ * core/tree-sitter/vendored-grammars.ts / #2111). Each ships committed platform
+ * prebuilds activated via node-gyp-build. All can be skipped via
  * GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 (postinstall scripts), or can silently
- * soft-fail when the toolchain is missing (Dart/Proto), when no prebuild
- * matches the host platform (Swift), or when the optional install was
- * skipped or its native build failed (Kotlin).
+ * soft-fail when no prebuild matches the host platform (and a source build was
+ * unavailable / not attempted).
  *
  * Either path produces the same observable: the .node binding is absent
  * at runtime. This helper detects that condition and surfaces a single

package/dist/cli/optional-grammars.js

@@ -1,26 +1,23 @@
 /**
  * Optional grammar availability check.
  *
- * tree-sitter-dart, tree-sitter-proto, and tree-sitter-swift are vendored
- * under vendor/ and materialized into node_modules/ at postinstall. Dart
- * and Proto are built from source with node-gyp; Swift ships platform
- * prebuilds activated via node-gyp-build. tree-sitter-kotlin is a declared
- * optionalDependency (not vendored). All can be skipped via
+ * tree-sitter-dart, -proto, -swift, and -kotlin are vendored under vendor/ and
+ * loaded from there by absolute path (NEVER copied into node_modules — see
+ * core/tree-sitter/vendored-grammars.ts / #2111). Each ships committed platform
+ * prebuilds activated via node-gyp-build. All can be skipped via
  * GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1 (postinstall scripts), or can silently
- * soft-fail when the toolchain is missing (Dart/Proto), when no prebuild
- * matches the host platform (Swift), or when the optional install was
- * skipped or its native build failed (Kotlin).
+ * soft-fail when no prebuild matches the host platform (and a source build was
+ * unavailable / not attempted).
  *
  * Either path produces the same observable: the .node binding is absent
  * at runtime. This helper detects that condition and surfaces a single
  * stderr line per missing grammar so users learn why .dart/.proto/.swift/.kt
  * support is unavailable instead of silently getting a degraded index.
  */
-import { createRequire } from 'module';
 import { SupportedLanguages } from '../_shared/index.js';
 import { isGrammarRuntimeSkipped } from '../core/tree-sitter/parser-loader.js';
+import { requireVendoredGrammar } from '../core/tree-sitter/vendored-grammars.js';
 import { cliWarn } from './cli-message.js';
-const _require = createRequire(import.meta.url);
 const OPTIONAL_GRAMMARS = [
     {
         name: 'tree-sitter-dart',
@@ -76,7 +73,7 @@ export function detectMissingOptionalGrammars() {
             continue;
         }
         try {
-            _require(g.pkg);
+            requireVendoredGrammar(g.pkg);
         }
         catch (err) {
             const code = err?.code;

package/dist/cli/skill-gen.js

@@ -485,6 +485,7 @@ const renderSkillMarkdown = (community, projectName, members, files, entryPoints
     lines.push(`1. \`context({name: "${firstEntry}"})\` \u2014 see callers and callees`);
     lines.push(`2. \`query({query: "${community.label.toLowerCase()}"})\` \u2014 find related execution flows`);
     lines.push('3. Read key files listed above for implementation details');
+    lines.push('4. `explain({target: "<file or symbol>"})` — persisted taint findings (source→sink data flows), when indexed with `--pdg`');
     lines.push('');
     return lines.join('\n');
 };

package/dist/cli/status.js

@@ -3,8 +3,9 @@
  *
  * Shows the indexing status of the current repository.
  */
-import { findRepo, getStoragePaths, hasKuzuIndex } from '../storage/repo-manager.js';
-import { getCurrentCommit, isGitRepo, getGitRoot } from '../storage/git.js';
+import path from 'path';
+import { findRepo, getStoragePaths, loadMeta, hasKuzuIndex } from '../storage/repo-manager.js';
+import { getCurrentCommit, getCurrentBranch, isGitRepo, getGitRoot } from '../storage/git.js';
 import { t } from './i18n/index.js';
 export const statusCommand = async () => {
     const cwd = process.cwd();
@@ -28,10 +29,30 @@ export const statusCommand = async () => {
         return;
     }
     const currentCommit = getCurrentCommit(repo.repoPath);
-    const isUpToDate = currentCommit === repo.meta.lastCommit;
+    const currentBranch = getCurrentBranch(repo.repoPath);
+    // Pick the index matching the checked-out branch (#2106). The flat index
+    // belongs to the primary branch (repo.meta.branch); when the current branch
+    // differs and has its own index, report that one. Legacy/no-branch metas and
+    // detached HEAD fall through to the flat index (unchanged behavior).
+    let activeMeta = repo.meta;
+    let currentBranchIndexed = true;
+    if (currentBranch && repo.meta.branch && currentBranch !== repo.meta.branch) {
+        const { metaPath } = getStoragePaths(repo.repoPath, currentBranch);
+        const branchMeta = await loadMeta(path.dirname(metaPath));
+        if (branchMeta)
+            activeMeta = branchMeta;
+        else
+            currentBranchIndexed = false;
+    }
     console.log(`${t('status.repository')}: ${repo.repoPath}`);
-    console.log(`${t('status.indexed')}: ${new Date(repo.meta.indexedAt).toLocaleString()}`);
-    console.log(`${t('status.indexedCommit')}: ${repo.meta.lastCommit?.slice(0, 7)}`);
+    console.log(`${t('status.branch')}: ${currentBranch ?? t('status.detached')}`);
+    if (!currentBranchIndexed) {
+        console.log(`${t('status.status')}: ${t('status.branchNotIndexed', { primary: repo.meta.branch ?? '' })}`);
+        return;
+    }
+    const isUpToDate = currentCommit === activeMeta.lastCommit;
+    console.log(`${t('status.indexed')}: ${new Date(activeMeta.indexedAt).toLocaleString()}`);
+    console.log(`${t('status.indexedCommit')}: ${activeMeta.lastCommit?.slice(0, 7)}`);
     console.log(`${t('status.currentCommit')}: ${currentCommit?.slice(0, 7)}`);
     console.log(`${t('status.status')}: ${isUpToDate ? t('status.upToDate') : t('status.stale')}`);
 };

package/dist/cli/tool.d.ts

@@ -1,7 +1,7 @@
 /**
  * Direct CLI Tool Commands
  *
- * Exposes GitNexus tools (query, context, impact, cypher) as direct CLI commands.
+ * Exposes GitNexus tools (query, context, impact, cypher, check) as direct CLI commands.
  * Bypasses MCP entirely — invokes LocalBackend directly for minimal overhead.
  *
  * Usage:
@@ -16,6 +16,7 @@
  */
 export declare function queryCommand(queryText: string, options?: {
     repo?: string;
+    branch?: string;
     context?: string;
     goal?: string;
     limit?: string;
@@ -23,6 +24,7 @@ export declare function queryCommand(queryText: string, options?: {
 }): Promise<void>;
 export declare function contextCommand(name: string, options?: {
     repo?: string;
+    branch?: string;
     file?: string;
     uid?: string;
     content?: boolean;
@@ -30,6 +32,7 @@ export declare function contextCommand(name: string, options?: {
 export declare function impactCommand(target?: string, options?: {
     direction?: string;
     repo?: string;
+    branch?: string;
     uid?: string;
     file?: string;
     kind?: string;
@@ -41,9 +44,17 @@ export declare function impactCommand(target?: string, options?: {
 }): Promise<void>;
 export declare function cypherCommand(query: string, options?: {
     repo?: string;
+    branch?: string;
 }): Promise<void>;
 export declare function detectChangesCommand(options?: {
     scope?: string;
     baseRef?: string;
     repo?: string;
+    branch?: string;
+}): Promise<void>;
+export declare function checkCommand(options?: {
+    cycles?: boolean;
+    json?: boolean;
+    repo?: string;
+    branch?: string;
 }): Promise<void>;

package/dist/cli/tool.js

@@ -1,7 +1,7 @@
 /**
  * Direct CLI Tool Commands
  *
- * Exposes GitNexus tools (query, context, impact, cypher) as direct CLI commands.
+ * Exposes GitNexus tools (query, context, impact, cypher, check) as direct CLI commands.
  * Bypasses MCP entirely — invokes LocalBackend directly for minimal overhead.
  *
  * Usage:
@@ -68,6 +68,7 @@ export async function queryCommand(queryText, options) {
         limit: options?.limit ? parseInt(options.limit) : undefined,
         include_content: options?.content ?? false,
         repo: options?.repo,
+        branch: options?.branch,
     });
     output(result);
 }
@@ -88,6 +89,7 @@ export async function contextCommand(name, options) {
         file_path: options?.file,
         include_content: options?.content ?? false,
         repo: options?.repo,
+        branch: options?.branch,
     });
     output(result);
 }
@@ -126,6 +128,7 @@ export async function impactCommand(target, options) {
             maxDepth: options?.depth ? parseInt(options.depth, 10) : undefined,
             includeTests: options?.includeTests ?? false,
             repo: options?.repo,
+            branch: options?.branch,
             limit: parsedLimit,
             offset: parsedOffset,
             summaryOnly: options?.summaryOnly ?? undefined,
@@ -153,6 +156,7 @@ export async function cypherCommand(query, options) {
     const result = await backend.callTool('cypher', {
         query,
         repo: options?.repo,
+        branch: options?.branch,
     });
     output(result);
 }
@@ -162,6 +166,42 @@ export async function detectChangesCommand(options) {
         scope: options?.scope || 'unstaged',
         base_ref: options?.baseRef,
         repo: options?.repo,
+        branch: options?.branch,
     });
     output(formatDetectChangesResult(result));
 }
+export async function checkCommand(options) {
+    if (!options?.cycles) {
+        process.stderr.write('Usage: gitnexus check --cycles [--json]\n');
+        process.exitCode = 1;
+        return;
+    }
+    try {
+        const backend = await getBackend();
+        const result = await backend.callTool('check', {
+            cycles: true,
+            repo: options.repo,
+            branch: options.branch,
+        });
+        if (result?.error) {
+            output(result);
+            process.exitCode = 1;
+            return;
+        }
+        if (options.json) {
+            output(result);
+        }
+        else if (result.cycleCount === 0) {
+            output('No circular imports found.');
+        }
+        else {
+            output(result.cycles.map((cycle) => cycle.files.join(' -> ')).join('\n'));
+        }
+        if (result.cycleCount > 0)
+            process.exitCode = 1;
+    }
+    catch (error) {
+        output({ error: error instanceof Error ? error.message : String(error) });
+        process.exitCode = 1;
+    }
+}

package/dist/core/embeddings/embedder.js

@@ -21,6 +21,7 @@ import { isHttpMode, getHttpDimensions, httpEmbed } from './http-client.js';
 import { resolveEmbeddingConfig } from './config.js';
 import { applyHfEnvOverrides, isHfDownloadFailure, withHfDownloadRetry } from './hf-env.js';
 import { getLocalEmbeddingRuntimeBlocker } from './runtime-support.js';
+import { ensureOnnxRuntimeCommonResolvable } from './onnxruntime-common-resolver.js';
 import { logger } from '../logger.js';
 /**
  * Check whether the onnxruntime-node package that @huggingface/transformers
@@ -147,6 +148,9 @@ export const initEmbedder = async (onProgress, config = {}, forceDevice) => {
         try {
             // Lazy-load transformers.js only after the runtime guard has passed, so
             // unsupported platforms never reach the native ONNX import (#1515).
+            // Under pnpm-strict / `pnpm dlx`, transformers' phantom `onnxruntime-common`
+            // import is unresolvable; register the fallback resolver first (#307).
+            ensureOnnxRuntimeCommonResolvable();
             const { pipeline, env } = await import('@huggingface/transformers');
             // Configure transformers.js environment
             env.allowLocalModels = false;