gitnexus 1.6.13-rc.36 → 1.6.13-rc.37

package/README.md

@@ -367,7 +367,7 @@ projects:
       - git@gitee.com:owner/repo.git
 ```
 
-`sync_interval_minutes` must be an integer of at least `5`. `local_path` must be an absolute path without traversal; each remote is cloned below it as `host/namespace/repo`, preventing same-basename repositories from colliding. `remote_urls` must use SSH SCP form for github.com, gitlab.com, or gitee.com. `repo_git_timeout` applies to each repo clone/pull and defaults to `10s`; a bare number such as `10` is interpreted as seconds, while `10000ms`, `10s`, and `1m` keep their explicit units. It must not exceed one hour or `sync_interval_minutes`, whichever is smaller — so a bare `600000` is rejected, because it means 600000 seconds rather than milliseconds. `analyze_timeout` applies to each isolated analysis worker and defaults to half of `sync_interval_minutes`, but it is independent of polling and may be longer, up to Node's timer limit (`2147483647ms`). A `5` minute poll with `analyze_timeout: 30m` is valid. A tick that arrives while the previous loop is active never overlaps it: ticks coalesce into one immediate follow-up run, which pulls and analyzes the newest commit. If the parent times out and leaves that worker running, the follow-up is deferred to the next interval so a leftover lock holder is not counted as a hard analyze failure. Timeout and `auto-sync stop` request safe cancellation; a worker already in native work exits after it returns to a JS-visible safe point. While waiting, auto-sync reports `cancelling` or `stopping` and keeps its ownership files so another auto-sync cannot take over. The parent waits up to 5 seconds for the worker to exit; after that it stops waiting, releases its ownership files, and leaves the worker to finish and exit on its own rather than killing it mid-write. `auto-sync stop` uses this same control path on macOS and Windows.
+`sync_interval_minutes` must be an integer of at least `5`. `local_path` must be an absolute path without traversal; each remote is cloned below it as `host/namespace/repo`, preventing same-basename repositories from colliding. `remote_urls` may use SSH SCP form (`git@host:owner/repo.git`) or HTTPS (`https://host/owner/repo.git`) for github.com, gitlab.com, or gitee.com. The published CLI image includes `openssh-client` so SSH remotes can clone; mount keys and `known_hosts` yourself. An invalid `watch_config.yml` skips auto-sync immediately with the validation error. `repo_git_timeout` applies to each repo clone/pull and defaults to `10s`; a bare number such as `10` is interpreted as seconds, while `10000ms`, `10s`, and `1m` keep their explicit units. It must not exceed one hour or `sync_interval_minutes`, whichever is smaller — so a bare `600000` is rejected, because it means 600000 seconds rather than milliseconds. `analyze_timeout` applies to each isolated analysis worker and defaults to half of `sync_interval_minutes`, but it is independent of polling and may be longer, up to Node's timer limit (`2147483647ms`). A `5` minute poll with `analyze_timeout: 30m` is valid. Auto-sync analysis honors the cloned repo's `.gitnexusrc` embeddings settings; the CLI image still needs `GITNEXUS_EMBEDDING_URL` or a bind-mounted embedding stack because npm is stripped. A tick that arrives while the previous loop is active never overlaps it: ticks coalesce into one immediate follow-up run, which pulls and analyzes the newest commit. If the parent times out and leaves that worker running, the follow-up is deferred to the next interval so a leftover lock holder is not counted as a hard analyze failure. Timeout and `auto-sync stop` request safe cancellation; a worker already in native work exits after it returns to a JS-visible safe point. While waiting, auto-sync reports `cancelling` or `stopping` and keeps its ownership files so another auto-sync cannot take over. The parent waits up to 5 seconds for the worker to exit; after that it stops waiting, releases its ownership files, and leaves the worker to finish and exit on its own rather than killing it mid-write. `auto-sync stop` uses this same control path on macOS and Windows.
 
 `pdg` is configured per project. `pdg: true` builds and maintains the full CFG, control-dependence, reaching-definition, and taint layers on both initial and incremental analyses. Auto-sync requests staged atomic incremental publication where the analyzer supports it: the old graph remains available to readers until the replacement succeeds, and analysis errors are recorded while the old graph remains intact. Unsupported paths retain the analyzer's existing in-place behavior. Untouched configs that omit `pdg` preserve the existing index mode and cannot silently strip PDG data. Do not paste `pdg: false` from this example onto an existing watch file unless you intend to drop PDG. An explicit `pdg: false` disables PDG and emits a warning before a successful rebuild removes those layers. `overwrite_local_changes` defaults to `false`; a dirty local clone is skipped with an error log, while `true` allows branch fallback to replace local changes and additionally discards untracked files and directories in the clone after checkout — ignored paths, including GitNexus's own `.gitnexus/` storage, are preserved. `max_concurrency` defaults to `1` and is capped at runtime by `floor(availableMemoryGB / 2)` with a minimum of `1`; the effective value is printed at the start of each loop. Each analysis worker's heap cap is the machine-wide cap divided by the number of repositories analyzed in parallel, so concurrent workers share one memory budget instead of each claiming the whole machine. `analyze_failure_threshold` defaults to `3`, must be at least `2`, and pauses repeated failures only for the same repo branch, commit, and requested PDG mode; a new commit, a PDG mode change, or `gitnexus auto-sync reset` clears the block and allows analysis again. Repositories are registered and added to groups by their full remote identity (`host/namespace/repo`), so repositories with the same basename remain distinct. Use `branches` to try branches in order; legacy `branch` remains supported, but the two fields cannot be set together. If all branches are unavailable or time out, watch logs an error, records the repo status, and skips that repo for the loop. Leave `group_name` empty or omit it to skip group add/sync for that project; otherwise create the group first with `gitnexus group create <name>`. `$GITNEXUS_HOME/watch/project_commit_info.txt` is for inspection only; GitNexus stores machine state separately in `$GITNEXUS_HOME/watch/auto-sync-state.json`.
 

package/dist/cli/auto-sync.js

@@ -106,6 +106,8 @@ function defaultSyncConfig(localPath) {
         '    overwrite_local_changes: false',
         '    remote_urls:',
         '      - git@github.com:owner/repo.git',
+        '      # HTTPS remotes on github.com, gitlab.com, or gitee.com are also allowed',
+        '      # - https://github.com/owner/public-repo.git',
         '',
     ].join('\n');
 }

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

@@ -170,7 +170,7 @@ export declare const en: {
     readonly 'help.command.setup.description': 'One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder, Codex, Factory Droid';
     readonly 'help.command.uninstall.description': 'Reverse `setup`: remove GitNexus MCP entries, skills, and hooks from all detected editors';
     readonly 'help.command.autoSync.description': 'Control scheduled repository clone/pull and analysis from GITNEXUS_HOME/watch_config.yml';
-    readonly 'help.autoSync.details': '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: only SSH URLs on github.com, gitlab.com, and gitee.com are allowed.\nRuns once immediately, then repeats on sync_interval_minutes.';
+    readonly 'help.autoSync.details': '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: SSH or HTTPS URLs on github.com, gitlab.com, and gitee.com are allowed. Invalid watch_config.yml skips auto-sync immediately.\nRuns once immediately, then repeats on sync_interval_minutes.';
     readonly 'help.command.watch.description': 'Ambiguous: use `analyze --watch` for local files, or `auto-sync` for scheduled remotes';
     readonly 'help.watch.details': '\n`gitnexus watch` does not start a watcher.\n  Local working-tree incremental index:  gitnexus analyze --watch\n  Scheduled remote clone/pull + analyze: gitnexus auto-sync start\n';
     readonly 'error.watch.ambiguous': '`gitnexus watch` is ambiguous.\n  Local working-tree incremental index:  gitnexus analyze --watch\n  Scheduled remote clone/pull + analyze: gitnexus auto-sync start\n';

package/dist/cli/i18n/en.js

@@ -172,7 +172,7 @@ export const en = {
     'help.command.setup.description': 'One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder, Codex, Factory Droid',
     'help.command.uninstall.description': 'Reverse `setup`: remove GitNexus MCP entries, skills, and hooks from all detected editors',
     'help.command.autoSync.description': 'Control scheduled repository clone/pull and analysis from GITNEXUS_HOME/watch_config.yml',
-    'help.autoSync.details': '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: only SSH URLs on github.com, gitlab.com, and gitee.com are allowed.\nRuns once immediately, then repeats on sync_interval_minutes.',
+    'help.autoSync.details': '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: SSH or HTTPS URLs on github.com, gitlab.com, and gitee.com are allowed. Invalid watch_config.yml skips auto-sync immediately.\nRuns once immediately, then repeats on sync_interval_minutes.',
     'help.command.watch.description': 'Ambiguous: use `analyze --watch` for local files, or `auto-sync` for scheduled remotes',
     'help.watch.details': '\n`gitnexus watch` does not start a watcher.\n  Local working-tree incremental index:  gitnexus analyze --watch\n  Scheduled remote clone/pull + analyze: gitnexus auto-sync start\n',
     'error.watch.ambiguous': '`gitnexus watch` is ambiguous.\n  Local working-tree incremental index:  gitnexus analyze --watch\n  Scheduled remote clone/pull + analyze: gitnexus auto-sync start\n',

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

@@ -171,7 +171,7 @@ export declare const cliResources: {
         readonly 'help.command.setup.description': 'One-time setup: configure MCP for Cursor, Claude Code, Antigravity, OpenCode, CodeBuddy, Qoder, Codex, Factory Droid';
         readonly 'help.command.uninstall.description': 'Reverse `setup`: remove GitNexus MCP entries, skills, and hooks from all detected editors';
         readonly 'help.command.autoSync.description': 'Control scheduled repository clone/pull and analysis from GITNEXUS_HOME/watch_config.yml';
-        readonly 'help.autoSync.details': '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: only SSH URLs on github.com, gitlab.com, and gitee.com are allowed.\nRuns once immediately, then repeats on sync_interval_minutes.';
+        readonly 'help.autoSync.details': '\nActions: init, start (default), restart, stop, status, reset\nConfiguration: GITNEXUS_HOME/watch_config.yml\nRuntime files: GITNEXUS_HOME/watch/watch.pid, watch.mutex, watch.owner.json, watch.status.json, auto-sync-state.json\nRecovery: mutexes with verified dead owners are reclaimed automatically; invalid or legacy mutexes fail closed and require manual removal after confirming no watch process is running.\nWrites: GITNEXUS_HOME/watch/project_commit_info.txt\nRemote URLs: SSH or HTTPS URLs on github.com, gitlab.com, and gitee.com are allowed. Invalid watch_config.yml skips auto-sync immediately.\nRuns once immediately, then repeats on sync_interval_minutes.';
         readonly 'help.command.watch.description': 'Ambiguous: use `analyze --watch` for local files, or `auto-sync` for scheduled remotes';
         readonly 'help.watch.details': '\n`gitnexus watch` does not start a watcher.\n  Local working-tree incremental index:  gitnexus analyze --watch\n  Scheduled remote clone/pull + analyze: gitnexus auto-sync start\n';
         readonly 'error.watch.ambiguous': '`gitnexus watch` is ambiguous.\n  Local working-tree incremental index:  gitnexus analyze --watch\n  Scheduled remote clone/pull + analyze: gitnexus auto-sync start\n';

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

@@ -170,7 +170,7 @@ export const zhCN = {
     'help.command.setup.description': '一次性设置：为 Cursor、Claude Code、Antigravity、OpenCode、CodeBuddy、Qoder、Codex、Factory Droid 配置 MCP',
     'help.command.uninstall.description': '撤销 `setup`：从所有检测到的编辑器中移除 GitNexus 的 MCP 配置、技能和钩子',
     'help.command.autoSync.description': '控制基于 GITNEXUS_HOME/watch_config.yml 的定时 clone/pull 和分析',
-    'help.autoSync.details': '\n操作：init、start（默认）、restart、stop、status、reset\n配置：GITNEXUS_HOME/watch_config.yml\n运行时文件：GITNEXUS_HOME/watch/watch.pid、watch.mutex、watch.owner.json、watch.status.json、auto-sync-state.json\n恢复：已验证 owner 退出的 mutex 会自动回收；无效或旧版 mutex 会安全拒绝，确认没有 watch 进程运行后再手动删除。\n写入：GITNEXUS_HOME/watch/project_commit_info.txt\n远程地址：仅允许 github.com、gitlab.com 和 gitee.com 上的 SSH 地址。\n启动后立即运行一次，之后按 sync_interval_minutes 重复。',
+    'help.autoSync.details': '\n操作：init、start（默认）、restart、stop、status、reset\n配置：GITNEXUS_HOME/watch_config.yml\n运行时文件：GITNEXUS_HOME/watch/watch.pid、watch.mutex、watch.owner.json、watch.status.json、auto-sync-state.json\n恢复：已验证 owner 退出的 mutex 会自动回收；无效或旧版 mutex 会安全拒绝，确认没有 watch 进程运行后再手动删除。\n写入：GITNEXUS_HOME/watch/project_commit_info.txt\n远程地址：允许 github.com、gitlab.com 和 gitee.com 上的 SSH 或 HTTPS 地址。无效的 watch_config.yml 会立即跳过 auto-sync。\n启动后立即运行一次，之后按 sync_interval_minutes 重复。',
     'help.command.watch.description': '含义不明确：本地文件请用 `analyze --watch`，定时远程同步请用 `auto-sync`',
     'help.watch.details': '\n`gitnexus watch` 不会启动监视器。\n  本地工作区增量索引：gitnexus analyze --watch\n  定时远程 clone/pull 并分析：gitnexus auto-sync start\n',
     'error.watch.ambiguous': '`gitnexus watch` 含义不明确。\n  本地工作区增量索引：gitnexus analyze --watch\n  定时远程 clone/pull 并分析：gitnexus auto-sync start\n',

package/dist/core/auto-sync/config.d.ts

@@ -30,6 +30,12 @@ export declare function getAutoSyncConfigPath(gitnexusDir?: string): string;
 export declare function parseBranchCandidates(branchValue: unknown): string[];
 export declare function loadAutoSyncConfig(configPath?: string): Promise<AutoSyncConfigLoadResult>;
 export declare function parseAutoSyncConfig(content: string, configPath: string): AutoSyncConfig;
+export declare function parseAutoSyncRemoteIdentity(remoteUrl: string): {
+    host: string;
+    repoPath: string;
+};
+/** Canonical `host/owner/repo` key. Strips one trailing `.git`. Throws on an invalid remote. */
+export declare function getAutoSyncRepoIdentity(remoteUrl: string): string;
 export declare function validateAutoSyncRemoteUrl(remoteUrl: string): void;
 export declare function validateAutoSyncBranchName(branch: string): void;
 export declare function parseDurationMs(value: unknown): number;

package/dist/core/auto-sync/config.js

@@ -237,17 +237,42 @@ export function parseAutoSyncConfig(content, configPath) {
         projects,
     };
 }
-export function validateAutoSyncRemoteUrl(remoteUrl) {
+export function parseAutoSyncRemoteIdentity(remoteUrl) {
     const trimmed = remoteUrl.trim();
     if (trimmed.includes('?') || trimmed.includes('#')) {
         throw new Error('must not include query strings or fragments');
     }
-    const match = /^git@([^:\s/]+):([^\s]+)$/.exec(trimmed);
-    if (!match) {
-        throw new Error('must use an SSH URL on github.com, gitlab.com, or gitee.com');
+    const sshMatch = /^git@([^:\s/]+):([^\s]+)$/.exec(trimmed);
+    const httpsMatch = /^https:\/\/([^/\s]+)\/([^\s]+)$/.exec(trimmed);
+    let host;
+    let repoPath;
+    if (sshMatch) {
+        host = sshMatch[1];
+        repoPath = sshMatch[2];
+    }
+    else if (httpsMatch) {
+        host = httpsMatch[1];
+        repoPath = httpsMatch[2];
+        if (host.includes('@') || host.includes(':')) {
+            throw new Error('must not include userinfo or a port');
+        }
+    }
+    else {
+        throw new Error('must use an SSH or HTTPS URL on github.com, gitlab.com, or gitee.com');
     }
-    const host = match[1].toLowerCase();
-    const repoPath = match[2];
+    host = host.toLowerCase();
+    assertAutoSyncRemotePath(host, repoPath);
+    return { host, repoPath };
+}
+/** Canonical `host/owner/repo` key. Strips one trailing `.git`. Throws on an invalid remote. */
+export function getAutoSyncRepoIdentity(remoteUrl) {
+    const { host, repoPath } = parseAutoSyncRemoteIdentity(remoteUrl);
+    return `${host}/${repoPath.replace(/\.git$/i, '')}`;
+}
+export function validateAutoSyncRemoteUrl(remoteUrl) {
+    parseAutoSyncRemoteIdentity(remoteUrl);
+}
+function assertAutoSyncRemotePath(host, repoPath) {
     if (!ALLOWED_REMOTE_HOSTS.has(host)) {
         throw new Error('host must be one of github.com, gitlab.com, or gitee.com');
     }

package/dist/core/auto-sync/index.d.ts

@@ -1,4 +1,4 @@
-export { AUTO_SYNC_CONFIG_FILE, getAutoSyncConfigPath, loadAutoSyncConfig, parseAutoSyncConfig, parseBranchCandidates, parseDurationMs, validateAutoSyncBranchName, validateAutoSyncRemoteUrl, type AutoSyncConfig, type AutoSyncConfigLoadResult, type AutoSyncProjectConfig, } from './config.js';
+export { AUTO_SYNC_CONFIG_FILE, getAutoSyncConfigPath, loadAutoSyncConfig, parseAutoSyncConfig, parseBranchCandidates, parseDurationMs, validateAutoSyncBranchName, validateAutoSyncRemoteUrl, parseAutoSyncRemoteIdentity, type AutoSyncConfig, type AutoSyncConfigLoadResult, type AutoSyncProjectConfig, } from './config.js';
 export { buildStateKey, getAutoSyncMutexPath, getAutoSyncWatchDir, getAutoSyncStatePath, getProjectCommitInfoPath, loadAutoSyncState, resetAutoSyncState, saveAutoSyncState, shouldAnalyzeCommit, writeProjectCommitInfo, type AutoSyncAnalyzeStatus, type AutoSyncCommitState, type AutoSyncCommitStateEntry, type ProjectCommitInfoEntry, } from './state.js';
 export { extractRepoNameFromRemoteUrl } from './repo.js';
 export { normalizeConfiguredCloneRoot, quarantineAutoSyncPartial, resolveConfiguredCloneRoot, type AutoSyncCloneRoot, } from './path-security.js';

package/dist/core/auto-sync/index.js

@@ -1,4 +1,4 @@
-export { AUTO_SYNC_CONFIG_FILE, getAutoSyncConfigPath, loadAutoSyncConfig, parseAutoSyncConfig, parseBranchCandidates, parseDurationMs, validateAutoSyncBranchName, validateAutoSyncRemoteUrl, } from './config.js';
+export { AUTO_SYNC_CONFIG_FILE, getAutoSyncConfigPath, loadAutoSyncConfig, parseAutoSyncConfig, parseBranchCandidates, parseDurationMs, validateAutoSyncBranchName, validateAutoSyncRemoteUrl, parseAutoSyncRemoteIdentity, } from './config.js';
 export { buildStateKey, getAutoSyncMutexPath, getAutoSyncWatchDir, getAutoSyncStatePath, getProjectCommitInfoPath, loadAutoSyncState, resetAutoSyncState, saveAutoSyncState, shouldAnalyzeCommit, writeProjectCommitInfo, } from './state.js';
 export { extractRepoNameFromRemoteUrl } from './repo.js';
 export { normalizeConfiguredCloneRoot, quarantineAutoSyncPartial, resolveConfiguredCloneRoot, } from './path-security.js';

package/dist/core/auto-sync/runner.d.ts

@@ -42,6 +42,6 @@ export declare function runAutoSyncOnce(config: AutoSyncConfig, options?: {
 }): Promise<AutoSyncRunResult>;
 export declare function getConfiguredRepoPath(project: Pick<AutoSyncProjectConfig, 'localPath'>, repoName: string, remoteUrl?: string): string;
 export declare function addRepoToGroup(project: Pick<AutoSyncProjectConfig, 'groupName'>, groupPath: string, registryName?: string): Promise<boolean>;
-export declare function getAutoSyncRepoIdentity(remoteUrl: string): string;
+export { getAutoSyncRepoIdentity } from './config.js';
 export declare function syncGroupByName(groupName: string): Promise<void>;
 export declare function resolveActualConcurrency(configured: number, availableMemoryGB: number): number;

package/dist/core/auto-sync/runner.js

@@ -5,11 +5,12 @@ import { loadGroupConfig } from '../group/config-parser.js';
 import { getDefaultGitnexusDir, getGroupDir } from '../group/storage.js';
 import { syncGroup } from '../group/sync.js';
 import { getStoragePaths, loadMeta, registerRepo, resolveBranchPlacement, } from '../../storage/repo-manager.js';
+import { embeddingsFromGitnexusRc } from '../gitnexus-rc-embeddings.js';
+import { getAutoSyncRepoIdentity } from './config.js';
 import { extractRepoNameFromRemoteUrl } from './repo.js';
 import { cloneOrPull, runGit } from '../../server/git-clone.js';
 import { resolveConfiguredCloneRoot } from './path-security.js';
 import { buildStateKey, loadAutoSyncState, saveAutoSyncState, shouldAnalyzeCommit, writeProjectCommitInfo, } from './state.js';
-import { validateAutoSyncRemoteUrl } from './config.js';
 import { AutoSyncAnalysisError, runAutoSyncAnalysis, } from './analysis-worker-launch.js';
 const _require = createRequire(import.meta.url);
 const yaml = _require('js-yaml');
@@ -149,6 +150,7 @@ export async function runAutoSyncOnce(config, options = {}) {
                     previousStatus: previous?.lastAnalyzeStatus,
                 })) {
                 try {
+                    const rcEmbeddings = await embeddingsFromGitnexusRc(targetDir);
                     const analysis = await deps.runAnalysis(targetDir, {
                         branch: currentBranch,
                         skipAgentsMd: true,
@@ -157,6 +159,7 @@ export async function runAutoSyncOnce(config, options = {}) {
                             ? { preserveExistingPdg: true }
                             : { pdg: requestedPdg }),
                         atomicIncremental: true,
+                        ...rcEmbeddings,
                     }, config.analyzeTimeoutMs, options.signal, options.onAnalysisCancellationRequested, analysisParallelism);
                     throwIfAborted(options.signal);
                     stats = analysis.stats;
@@ -386,11 +389,7 @@ export async function addRepoToGroup(project, groupPath, registryName = groupPat
     await writeGroupConfigAtomic(path.join(groupDir, 'group.yaml'), config);
     return true;
 }
-export function getAutoSyncRepoIdentity(remoteUrl) {
-    validateAutoSyncRemoteUrl(remoteUrl);
-    const [, host, remotePath] = /^git@([^:\s/]+):([^\s]+)$/.exec(remoteUrl.trim());
-    return `${host.toLowerCase()}/${remotePath.replace(/\.git$/i, '')}`;
-}
+export { getAutoSyncRepoIdentity } from './config.js';
 export async function syncGroupByName(groupName) {
     const groupDir = getGroupDir(getDefaultGitnexusDir(), groupName);
     const config = await loadGroupConfig(groupDir);

package/dist/core/gitnexus-rc-embeddings.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Auto-sync reads embeddings settings from a cloned repo's `.gitnexusrc`
+ * without importing CLI modules (`src/core` must not import `src/cli`).
+ * Invalid JSON fails the analyze for that repo the same way CLI analyze fails closed.
+ */
+import type { AnalyzeOptions } from './run-analyze.js';
+export declare const GITNEXUS_RC_FILENAME = ".gitnexusrc";
+export declare class AutoSyncGitnexusRcError extends Error {
+    constructor(message: string);
+}
+export declare function embeddingsFromGitnexusRc(repoRoot: string): Promise<Pick<AnalyzeOptions, 'embeddings' | 'embeddingsNodeLimit'>>;

package/dist/core/gitnexus-rc-embeddings.js

@@ -0,0 +1,51 @@
+import { readRepoControlFile } from '../config/repo-control-file.js';
+export const GITNEXUS_RC_FILENAME = '.gitnexusrc';
+export class AutoSyncGitnexusRcError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = 'AutoSyncGitnexusRcError';
+    }
+}
+export async function embeddingsFromGitnexusRc(repoRoot) {
+    let raw;
+    try {
+        raw = await readRepoControlFile(repoRoot, GITNEXUS_RC_FILENAME);
+    }
+    catch (err) {
+        throw new AutoSyncGitnexusRcError(`Could not read ${GITNEXUS_RC_FILENAME}: ${err.message}`);
+    }
+    if (raw === null)
+        return {};
+    if (raw.charCodeAt(0) === 0xfeff)
+        raw = raw.slice(1);
+    let parsed;
+    try {
+        parsed = JSON.parse(raw);
+    }
+    catch {
+        throw new AutoSyncGitnexusRcError(`${GITNEXUS_RC_FILENAME} is not valid JSON`);
+    }
+    if (parsed === null || typeof parsed !== 'object' || Array.isArray(parsed)) {
+        throw new AutoSyncGitnexusRcError(`${GITNEXUS_RC_FILENAME} must contain a JSON object.`);
+    }
+    const obj = parsed;
+    let embeddingsVal = obj.embeddings;
+    if (obj.analyze && typeof obj.analyze === 'object' && !Array.isArray(obj.analyze)) {
+        const nested = obj.analyze;
+        if (Object.prototype.hasOwnProperty.call(nested, 'embeddings')) {
+            embeddingsVal = nested.embeddings;
+        }
+    }
+    if (embeddingsVal === undefined)
+        return {};
+    if (typeof embeddingsVal === 'boolean') {
+        return { embeddings: embeddingsVal };
+    }
+    if (typeof embeddingsVal === 'number') {
+        if (!Number.isInteger(embeddingsVal) || embeddingsVal < 0) {
+            throw new AutoSyncGitnexusRcError(`${GITNEXUS_RC_FILENAME} embeddings must be true/false or a non-negative integer`);
+        }
+        return { embeddings: true, embeddingsNodeLimit: embeddingsVal };
+    }
+    throw new AutoSyncGitnexusRcError(`${GITNEXUS_RC_FILENAME} embeddings must be a boolean or a non-negative integer`);
+}

package/dist/mcp/local/local-backend.d.ts

@@ -317,6 +317,7 @@ export declare class LocalBackend {
      * degradation is visible once instead of silent.
      */
     private warnedMissingEmbeddingStack;
+    private warnedNoEmbeddingVectors;
     /**
      * Width the semantic lane last produced a QUERY vector at for an index, keyed
      * by `lbugPath` (like `lastObservedPoolState`, and for the same reason: branch
@@ -622,6 +623,11 @@ export declare class LocalBackend {
      * BM25 keyword search helper - uses LadybugDB FTS for always-fresh results
      */
     private bm25Search;
+    /**
+     * Keyword-only indexes are the default. Do not put this on `query.warning`
+     * (that field is reserved for FTS/stack degradation). Log once per backend.
+     */
+    private logKeywordOnlyEmbeddings;
     /**
      * Semantic vector search helper
      */

package/dist/mcp/local/local-backend.js

@@ -1060,6 +1060,7 @@ export class LocalBackend {
      * degradation is visible once instead of silent.
      */
     warnedMissingEmbeddingStack = false;
+    warnedNoEmbeddingVectors = false;
     /**
      * Width the semantic lane last produced a QUERY vector at for an index, keyed
      * by `lbugPath` (like `lastObservedPoolState`, and for the same reason: branch
@@ -3043,6 +3044,16 @@ export class LocalBackend {
         }
         return { results, ftsUsed, ...(nonBenignErrors && { nonBenignErrors }) };
     }
+    /**
+     * Keyword-only indexes are the default. Do not put this on `query.warning`
+     * (that field is reserved for FTS/stack degradation). Log once per backend.
+     */
+    logKeywordOnlyEmbeddings() {
+        if (this.warnedNoEmbeddingVectors)
+            return;
+        this.warnedNoEmbeddingVectors = true;
+        logger.warn('GitNexus [query:vector]: This index has no embedding vectors — results are keyword-only. Enable embeddings in `.gitnexusrc` (auto-sync honors that file) or run `gitnexus analyze --embeddings`.');
+    }
     /**
      * Semantic vector search helper
      */
@@ -3057,10 +3068,8 @@ export class LocalBackend {
             // the count is read, to decide whether to load the embedding model at all.
             const tableCheck = await executeQuery(repo.lbugPath, `MATCH (e:${EMBEDDING_TABLE_NAME}) RETURN COUNT(*) AS cnt LIMIT 1`);
             if (!tableCheck.length || (tableCheck[0].cnt ?? tableCheck[0][0]) === 0) {
-                // No vectors to search: nothing is embedded below, so drop any width a
-                // previous call recorded rather than let query() warn about a lane that
-                // did not run this time (#2798).
                 this.lastQueryEmbeddingDims.delete(repo.lbugPath);
+                this.logKeywordOnlyEmbeddings();
                 return [];
             }
             const { embedQuery, getEmbeddingDims } = await import('../core/embedder.js');
@@ -3204,6 +3213,9 @@ export class LocalBackend {
                 if (degraded)
                     degraded.reason = message;
             }
+            else if (isBenignMissingTableError(err)) {
+                this.logKeywordOnlyEmbeddings();
+            }
             if (!this.warnedMissingEmbeddingStack && isDegradedVectorError) {
                 this.warnedMissingEmbeddingStack = true;
                 logger.warn(`GitNexus [query:vector]: ${message}`);

package/dist/server/git-clone.d.ts

@@ -109,10 +109,9 @@ export declare function normalizeGitUrlForCompare(url: string): string;
 /**
  * Read `remote.origin.url` from an existing clone using `git config --get`.
  *
- * Returns `null` if the config key is absent, the spawn fails, or the
- * directory isn't a git repository. The caller decides what a missing
- * remote means for its threat model — for cloneOrPull, a missing remote
- * on an existing clone is treated as a refuse-to-pull condition.
+ * Returns `null` only when the key is absent (exit 1) or empty. Timeouts and
+ * every other git failure throw, so a lock or spawn error is not treated as
+ * a missing origin.
  */
 export declare function getRemoteOriginUrl(cwd: string, timeoutMs?: number): Promise<string | null>;
 /**
@@ -129,7 +128,7 @@ export declare function getRemoteOriginUrl(cwd: string, timeoutMs?: number): Pro
  * Exported so the comparison logic is testable in isolation against any
  * tmpdir-based fixture, without needing to populate CLONE_ROOT.
  */
-export declare function assertRemoteMatchesRequestedUrl(targetDir: string, requestedUrl: string, timeoutMs?: number): Promise<void>;
+export declare function assertRemoteMatchesRequestedUrl(targetDir: string, requestedUrl: string, timeoutMs?: number, knownOriginUrl?: string): Promise<void>;
 /**
  * Clone or pull a git repository.
  *

package/dist/server/git-clone.js

@@ -14,7 +14,7 @@ import { branchSlug } from '../storage/branch-index.js';
 import { sanitizeRepoName, stripUrlCredentials } from '../storage/git.js';
 import { validateGitUrl } from '../core/net/url-guard.js';
 import { assertDirectoryOwnerAndPermissions, quarantineAutoSyncPartial, } from '../core/auto-sync/path-security.js';
-import { validateAutoSyncRemoteUrl } from '../core/auto-sync/config.js';
+import { getAutoSyncRepoIdentity, validateAutoSyncRemoteUrl } from '../core/auto-sync/config.js';
 export { validateGitUrl };
 /**
  * Root directory for all cloned repositories. Targets must resolve inside this.
@@ -272,13 +272,21 @@ export function normalizeGitUrlForCompare(url) {
         return trimmed.toLowerCase();
     }
 }
+/** Same allowlisted repo across SSH and HTTPS, ignoring a trailing `.git`. */
+function sameAllowlistedAutoSyncRepo(left, right) {
+    try {
+        return getAutoSyncRepoIdentity(left) === getAutoSyncRepoIdentity(right);
+    }
+    catch {
+        return false;
+    }
+}
 /**
  * Read `remote.origin.url` from an existing clone using `git config --get`.
  *
- * Returns `null` if the config key is absent, the spawn fails, or the
- * directory isn't a git repository. The caller decides what a missing
- * remote means for its threat model — for cloneOrPull, a missing remote
- * on an existing clone is treated as a refuse-to-pull condition.
+ * Returns `null` only when the key is absent (exit 1) or empty. Timeouts and
+ * every other git failure throw, so a lock or spawn error is not treated as
+ * a missing origin.
  */
 export async function getRemoteOriginUrl(cwd, timeoutMs) {
     try {
@@ -286,9 +294,12 @@ export async function getRemoteOriginUrl(cwd, timeoutMs) {
         return stdout.trim() || null;
     }
     catch (error) {
-        if (error.message.includes('timed out'))
+        const message = error.message ?? '';
+        if (message.includes('timed out'))
             throw error;
-        return null;
+        if (message.includes('failed (exit code 1)'))
+            return null;
+        throw error;
     }
 }
 /**
@@ -305,8 +316,8 @@ export async function getRemoteOriginUrl(cwd, timeoutMs) {
  * Exported so the comparison logic is testable in isolation against any
  * tmpdir-based fixture, without needing to populate CLONE_ROOT.
  */
-export async function assertRemoteMatchesRequestedUrl(targetDir, requestedUrl, timeoutMs) {
-    const remoteUrl = await getRemoteOriginUrl(targetDir, timeoutMs);
+export async function assertRemoteMatchesRequestedUrl(targetDir, requestedUrl, timeoutMs, knownOriginUrl) {
+    const remoteUrl = knownOriginUrl ?? (await getRemoteOriginUrl(targetDir, timeoutMs));
     if (remoteUrl === null) {
         throw new Error(`Existing clone at ${targetDir} has no remote.origin — refusing to pull`);
     }
@@ -477,17 +488,39 @@ export async function cloneOrPull(url, targetDir, onProgress, options) {
     await fs.mkdir(path.dirname(safeTarget), { recursive: true });
     await assertNoSymlinkPath(cloneRoot, safeTarget, Boolean(options?.allowedCloneRoot));
     await assertPreRealpathContainment(cloneRoot, safeTarget);
-    const exists = await fs.access(path.join(safeTarget, '.git')).then(() => true, () => false);
+    let exists = await fs.access(path.join(safeTarget, '.git')).then(() => true, () => false);
+    let originUrl = null;
+    if (exists && options?.allowAutoSyncSsh) {
+        originUrl = await getRemoteOriginUrl(safeTarget, options?.timeoutMs);
+        if (!originUrl) {
+            if (options.quarantineRoot) {
+                await quarantineAutoSyncPartial(safeTarget, options.quarantineRoot);
+                exists = false;
+            }
+            else {
+                throw new Error(`Existing clone at ${safeTarget} has no remote.origin — remove ${safeTarget} and retry`);
+            }
+        }
+    }
     const targetExists = await fs.access(safeTarget).then(() => true, () => false);
     if (exists) {
         if (options?.allowedCloneRoot) {
             await assertNoSymlinkPath(cloneRoot, path.join(safeTarget, '.git'), true);
         }
         await assertPostRealpathContainment(cloneRoot, safeTarget);
+        let originForCompare = originUrl;
+        if (originUrl &&
+            normalizeGitUrlForCompare(originUrl) !== normalizeGitUrlForCompare(url) &&
+            sameAllowlistedAutoSyncRepo(originUrl, url)) {
+            await runGit(['remote', 'set-url', 'origin', url], safeTarget, {
+                timeoutMs: options?.timeoutMs,
+            });
+            originForCompare = url;
+        }
         // Confirm the existing clone is actually the same repository the caller
         // requested. Without this check, a pull would silently succeed against
         // whatever remote the dir was originally cloned from.
-        await assertRemoteMatchesRequestedUrl(safeTarget, url, options?.timeoutMs);
+        await assertRemoteMatchesRequestedUrl(safeTarget, url, options?.timeoutMs, originForCompare ?? undefined);
         onProgress?.({ phase: 'pulling', message: 'Pulling latest changes...' });
         const runGitImpl = options?.runGitForTest ?? runGit;
         const gitOpts = {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.6.13-rc.36",
+  "version": "1.6.13-rc.37",
   "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",

package/scripts/cross-platform-tests.ts

@@ -341,6 +341,12 @@ const FILESYSTEM = [
   // 4893-file pass — 2.3 s on a slow virtualised filesystem, 0.34 s on a local
   // disk — against a 30 s testTimeout.
   'test/unit/source-control-bytes.test.ts',
+  // Auto-sync reads a cloned `.gitnexusrc` through the symlink/hard-link guard,
+  // and clone recovery uses real `git` plus temp dirs. Ubuntu coverage alone
+  // would never create the Windows file symlink (`type: 'file'`) or run the
+  // git-config failure path on windows-latest / macos-latest.
+  'test/unit/gitnexus-rc-embeddings.test.ts',
+  'test/unit/git-clone.test.ts',
 ];
 
 const ALL_CROSS_PLATFORM = [