grepmax 0.24.0 → 0.25.0

package/dist/commands/peek.js

@@ -52,6 +52,7 @@ const agent_errors_1 = require("../lib/utils/agent-errors");
 const exit_1 = require("../lib/utils/exit");
 const filter_builder_1 = require("../lib/utils/filter-builder");
 const language_1 = require("../lib/utils/language");
+const path_containment_1 = require("../lib/utils/path-containment");
 const project_registry_1 = require("../lib/utils/project-registry");
 const project_root_1 = require("../lib/utils/project-root");
 const stale_hint_1 = require("../lib/utils/stale-hint");
@@ -65,9 +66,9 @@ const style = {
 };
 const MAX_CALLERS = 5;
 const MAX_CALLEES = 8;
-function extractSignature(filePath, startLine, endLine) {
+function extractSignature(projectRoot, filePath, startLine, endLine) {
     try {
-        const content = fs.readFileSync(filePath, "utf-8");
+        const content = fs.readFileSync((0, path_containment_1.resolveContainedFile)(projectRoot, filePath), "utf-8");
         const lines = content.split("\n");
         const chunk = lines.slice(startLine, endLine + 1);
         const bodyLines = chunk.length;
@@ -249,7 +250,17 @@ exports.peek = new commander_1.Command("peek")
         // Re-anchor chunk-level caller rows to actual call sites and dedupe —
         // getCallers() returns one row per chunk, which multiplies callers for
         // classes split across many chunks (verified: 3 real call sites → 66).
-        const resolvedCallers = (0, callsites_1.resolveCallSites)(callerList, symbol).map((c) => {
+        const readableCallers = callerList.flatMap((caller) => {
+            try {
+                return [
+                    Object.assign(Object.assign({}, caller), { file: (0, path_containment_1.resolveContainedFile)(projectRoot, caller.file) }),
+                ];
+            }
+            catch (_a) {
+                return [];
+            }
+        });
+        const resolvedCallers = (0, callsites_1.resolveCallSites)(readableCallers, symbol).map((c) => {
             var _a;
             return ({
                 symbol: c.symbol,
@@ -294,7 +305,7 @@ exports.peek = new commander_1.Command("peek")
             }
             // Signature — all lines up to the opening brace, collapsed to one
             // line so parameters survive (first-line-only loses them).
-            const { signatureOnly } = extractSignature(center.file, startLine, endLine);
+            const { signatureOnly } = extractSignature(projectRoot, center.file, startLine, endLine);
             const sigOnly = signatureOnly
                 .split("\n")
                 .map((l) => l.trim())
@@ -340,7 +351,7 @@ exports.peek = new commander_1.Command("peek")
             }
             console.log();
             // Signature with collapsed body
-            const { signature } = extractSignature(center.file, startLine, endLine);
+            const { signature } = extractSignature(projectRoot, center.file, startLine, endLine);
             for (const line of signature.split("\n")) {
                 console.log(`  ${line}`);
             }

package/dist/commands/repair.js

@@ -1,37 +1,4 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
 var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
     function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
     return new (P || (P = Promise))(function (resolve, reject) {
@@ -41,50 +8,78 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.repair = void 0;
-const readline = __importStar(require("node:readline"));
 const commander_1 = require("commander");
-const ora_1 = __importDefault(require("ora"));
 const config_1 = require("../config");
 const index_config_1 = require("../lib/index/index-config");
 const vector_db_1 = require("../lib/store/vector-db");
+const daemon_client_1 = require("../lib/utils/daemon-client");
 const exit_1 = require("../lib/utils/exit");
 const project_registry_1 = require("../lib/utils/project-registry");
-function confirm(message) {
-    const rl = readline.createInterface({
-        input: process.stdin,
-        output: process.stdout,
-    });
-    return new Promise((resolve) => {
-        rl.question(`${message} [y/N] `, (answer) => {
-            rl.close();
-            resolve(answer.toLowerCase() === "y");
-        });
-    });
-}
+const REBUILD_PROTOCOL = 1;
 exports.repair = new commander_1.Command("repair")
     .description("Repair the centralized index (recover from a schema mismatch)")
-    .option("--rebuild", "Drop the shared vector table and re-index every project at the configured embedding dim", false)
-    .option("-y, --yes", "Skip the confirmation prompt", false)
+    .option("--rebuild", "Run the guarded exclusive whole-corpus generation rebuild", false)
     .addHelpText("after", `
 The shared LanceDB \`chunks\` table is fixed-width at creation. Switching model
 tiers (e.g. small 384d -> standard 768d) strands the table at the old width, so
 every write then fails. A per-project \`gmax index --reset\` only deletes rows —
-it can't change the table width. \`${config_1.REBUILD_COMMAND}\` drops the table and
-re-embeds all projects at the current dim.
+it can't change the table width. The guarded rebuild runs only through a daemon
+that advertises the exclusive-generation protocol; it never falls back to local
+store access.
 
 Examples:
-  gmax repair             Show schema status and what a rebuild would do
-  gmax repair --rebuild   Drop the table and re-index every project
-  gmax repair --rebuild -y  Rebuild without the confirmation prompt
+  gmax repair             Show schema status
+  gmax repair --rebuild   Rebuild every registered project at configured width
 `)
     .action((opts) => __awaiter(void 0, void 0, void 0, function* () {
     var _a, _b, _c;
     try {
+        if (opts.rebuild) {
+            const running = yield (0, daemon_client_1.ensureDaemonRunning)();
+            if (!running)
+                throw new Error("failed to start the gmax daemon");
+            const ping = yield (0, daemon_client_1.sendDaemonCommand)({ cmd: "ping" }, { timeoutMs: 10000 });
+            const capabilities = ping.capabilities && typeof ping.capabilities === "object"
+                ? ping.capabilities
+                : null;
+            if (!ping.ok ||
+                (capabilities === null || capabilities === void 0 ? void 0 : capabilities.exclusiveGenerationRebuild) !== REBUILD_PROTOCOL) {
+                throw new Error("running daemon does not support guarded rebuild protocol v1; restart the gmax daemon and retry");
+            }
+            const done = yield (0, daemon_client_1.sendStreamingCommand)({ cmd: "repair-v2", protocol: REBUILD_PROTOCOL }, (progress) => {
+                var _a;
+                const phase = String((_a = progress.phase) !== null && _a !== void 0 ? _a : "rebuild");
+                const project = typeof progress.project === "string"
+                    ? ` ${progress.project}`
+                    : "";
+                const counts = typeof progress.processed === "number" &&
+                    typeof progress.total === "number"
+                    ? ` ${progress.processed}/${progress.total}`
+                    : "";
+                const message = typeof progress.message === "string"
+                    ? `: ${progress.message}`
+                    : "";
+                console.log(`[${phase}]${project}${counts}${message}`);
+            }, { timeoutMs: 24 * 60 * 60 * 1000 });
+            if (!done.ok) {
+                const blockers = Array.isArray(done.blockers)
+                    ? ` Blockers: ${done.blockers
+                        .map((owner) => {
+                        var _a, _b;
+                        const value = owner;
+                        return `${(_a = value.role) !== null && _a !== void 0 ? _a : "unknown"} pid=${(_b = value.pid) !== null && _b !== void 0 ? _b : "?"}`;
+                    })
+                        .join(", ")}.`
+                    : "";
+                throw new Error(`${String((_a = done.error) !== null && _a !== void 0 ? _a : "rebuild failed")}.${blockers}`);
+            }
+            console.log(`Rebuild complete: ${String((_b = done.completed) !== null && _b !== void 0 ? _b : 0)}/${String((_c = done.total) !== null && _c !== void 0 ? _c : 0)} projects indexed.`);
+            if (typeof done.warning === "string")
+                console.warn(done.warning);
+            return;
+        }
         const globalConfig = (0, index_config_1.readGlobalConfig)();
         const configDim = globalConfig.vectorDim;
         // Physical width of the on-disk table (null if no table yet). Opened
@@ -106,74 +101,13 @@ Examples:
         console.log(dimLine);
         if (!opts.rebuild) {
             if (physicalDim != null && physicalDim !== configDim) {
-                console.log(`\nRun '${config_1.REBUILD_COMMAND}' to drop the table and re-index ` +
-                    `${projects.length} project(s) at ${configDim}d.`);
+                console.log(`\nRun ${config_1.REBUILD_COMMAND} to rebuild ${projects.length} project(s) at ${configDim}d.`);
             }
             else {
-                console.log(`\nNothing to repair. Pass --rebuild to force a full drop + re-index anyway.`);
-            }
-            return;
-        }
-        if (projects.length === 0) {
-            console.log("\nNo indexed projects to rebuild.");
-            return;
-        }
-        const totalChunks = projects.reduce((sum, p) => { var _a; return sum + ((_a = p.chunkCount) !== null && _a !== void 0 ? _a : 0); }, 0);
-        console.log(`\nThis will DROP the shared vector table and re-embed ${projects.length} project(s)` +
-            (totalChunks > 0
-                ? ` (~${totalChunks.toLocaleString()} chunks).`
-                : "."));
-        for (const p of projects) {
-            console.log(`  - ${p.name}`);
-        }
-        if (!opts.yes) {
-            const ok = yield confirm("\nContinue?");
-            if (!ok) {
-                console.log("Cancelled.");
-                return;
+                console.log("\nNo schema mismatch detected.");
             }
-        }
-        // The rebuild must run through the daemon — it is the single writer for
-        // the shared table. Refuse rather than risk a torn drop alongside a
-        // daemon mid-flush.
-        const { ensureDaemonRunning, sendStreamingCommand } = yield Promise.resolve().then(() => __importStar(require("../lib/utils/daemon-client")));
-        if (!(yield ensureDaemonRunning())) {
-            console.error("Could not start the gmax daemon. Start it with 'gmax watch --daemon -b' and retry.");
-            process.exitCode = 1;
             return;
         }
-        const spinner = (0, ora_1.default)({
-            text: "Dropping vector table...",
-            isSilent: !process.stdout.isTTY,
-        }).start();
-        try {
-            const done = yield sendStreamingCommand({ cmd: "repair" }, (msg) => {
-                var _a, _b, _c, _d;
-                if (msg.phase === "drop") {
-                    spinner.text = "Dropping vector table...";
-                }
-                else if (msg.phase === "reindex") {
-                    const doneN = (_a = msg.projectsDone) !== null && _a !== void 0 ? _a : 0;
-                    const totalN = (_b = msg.projectsTotal) !== null && _b !== void 0 ? _b : projects.length;
-                    const processed = (_c = msg.processed) !== null && _c !== void 0 ? _c : 0;
-                    const total = (_d = msg.total) !== null && _d !== void 0 ? _d : 0;
-                    const counts = total > 0 ? ` ${processed}/${total}` : "";
-                    spinner.text = `Re-indexing ${msg.project} (${doneN + 1}/${totalN})${counts}`;
-                }
-            });
-            if (!done.ok) {
-                spinner.fail("Rebuild failed");
-                throw new Error((_a = done.error) !== null && _a !== void 0 ? _a : "daemon repair failed");
-            }
-            const rebuilt = (_b = done.projects) !== null && _b !== void 0 ? _b : 0;
-            const indexed = (_c = done.indexed) !== null && _c !== void 0 ? _c : 0;
-            spinner.succeed(`Rebuilt ${rebuilt} project(s) at ${configDim}d • ${indexed.toLocaleString()} chunks`);
-        }
-        catch (e) {
-            if (spinner.isSpinning)
-                spinner.fail("Rebuild failed");
-            throw e;
-        }
     }
     catch (error) {
         const message = error instanceof Error ? error.message : "Unknown error";

package/dist/commands/search-output.js

@@ -51,6 +51,7 @@ const index_state_footer_1 = require("../lib/output/index-state-footer");
 const cross_project_1 = require("../lib/utils/cross-project");
 const formatter_1 = require("../lib/utils/formatter");
 const import_extractor_1 = require("../lib/utils/import-extractor");
+const path_containment_1 = require("../lib/utils/path-containment");
 const search_skeletons_1 = require("./search-skeletons");
 /**
  * Standalone HTTP-server search path. The per-project server answers the query
@@ -70,7 +71,7 @@ function executeServerSearch(params) {
     return __awaiter(this, void 0, void 0, function* () {
         const { server, pattern, exec_path, projectRootForServer, options, minScore, } = params;
         try {
-            const response = yield fetch(`http://localhost:${server.port}/search`, {
+            const response = yield fetch(`http://127.0.0.1:${server.port}/search`, {
                 method: "POST",
                 headers: { "Content-Type": "application/json" },
                 body: JSON.stringify({
@@ -79,6 +80,11 @@ function executeServerSearch(params) {
                     path: exec_path
                         ? path.relative(projectRootForServer, path.resolve(exec_path))
                         : undefined,
+                    in: options.in,
+                    exclude: options.exclude,
+                    file: options.file,
+                    lang: options.lang,
+                    role: options.role,
                 }),
             });
             if (response.ok) {
@@ -119,8 +125,15 @@ function executeServerSearch(params) {
                 }
                 if (options.agent) {
                     const importCache = new Map();
-                    const getImportsForFile = (absPath) => {
+                    const getImportsForFile = (indexedPath) => {
                         var _a;
+                        let absPath;
+                        try {
+                            absPath = (0, path_containment_1.resolveContainedFile)(projectRootForServer, indexedPath);
+                        }
+                        catch (_b) {
+                            return "";
+                        }
                         if (!options.imports || !absPath)
                             return "";
                         if (!importCache.has(absPath)) {
@@ -212,15 +225,23 @@ function renderSearchOutput(params) {
         }
         // Build import cache when --imports is requested
         const importCache = new Map();
-        const getImportsForFile = (absPath) => {
+        const getImportsForRoot = (root) => (indexedPath) => {
             var _a;
-            if (!options.imports || !absPath)
+            if (!options.imports || !indexedPath)
+                return "";
+            let absPath;
+            try {
+                absPath = (0, path_containment_1.resolveContainedFile)(root, indexedPath);
+            }
+            catch (_b) {
                 return "";
+            }
             if (!importCache.has(absPath)) {
                 importCache.set(absPath, (0, import_extractor_1.extractImports)(absPath));
             }
             return (_a = importCache.get(absPath)) !== null && _a !== void 0 ? _a : "";
         };
+        const getImportsForFile = getImportsForRoot(effectiveRoot);
         // Agent mode: ultra-compact one-line-per-result output
         const resultCount = filteredData.length;
         // Cross-project (Phase 6): render grouped by owning project so idioms
@@ -259,7 +280,7 @@ function renderSearchOutput(params) {
                     body = (0, agent_search_formatter_1.formatAgentSearchResults)(g.items, g.root, {
                         includeImports: options.imports,
                         query: pattern,
-                        getImportsForFile,
+                        getImportsForFile: getImportsForRoot(g.root),
                         explain: options.explain,
                     });
                 }
@@ -377,12 +398,10 @@ function renderSearchOutput(params) {
             // aborting the loop — recovering budget the old greedy `break` wasted.
             const candidates = filteredData.map((r, idx) => {
                 var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l;
-                const absP = (_c = (_a = r.path) !== null && _a !== void 0 ? _a : (_b = r.metadata) === null || _b === void 0 ? void 0 : _b.path) !== null && _c !== void 0 ? _c : "";
+                const indexedPath = (_c = (_a = r.path) !== null && _a !== void 0 ? _a : (_b = r.metadata) === null || _b === void 0 ? void 0 : _b.path) !== null && _c !== void 0 ? _c : "";
                 const startLine = (_g = (_e = (_d = r.startLine) !== null && _d !== void 0 ? _d : r.start_line) !== null && _e !== void 0 ? _e : (_f = r.generated_metadata) === null || _f === void 0 ? void 0 : _f.start_line) !== null && _g !== void 0 ? _g : 0;
                 const endLine = (_l = (_j = (_h = r.endLine) !== null && _h !== void 0 ? _h : r.end_line) !== null && _j !== void 0 ? _j : (_k = r.generated_metadata) === null || _k === void 0 ? void 0 : _k.end_line) !== null && _l !== void 0 ? _l : startLine;
-                const relPath = absP.startsWith(projectRoot)
-                    ? absP.slice(projectRoot.length + 1)
-                    : absP;
+                let relPath = "(invalid indexed path)";
                 const role = r.role || "IMPLEMENTATION";
                 const symbol = Array.isArray(r.defined_symbols) &&
                     r.defined_symbols.length > 0
@@ -390,6 +409,8 @@ function renderSearchOutput(params) {
                     : "";
                 let blobText;
                 try {
+                    const absP = (0, path_containment_1.resolveContainedFile)(projectRoot, indexedPath);
+                    relPath = path.relative(fs.realpathSync(projectRoot), absP);
                     const content = fs.readFileSync(absP, "utf-8");
                     const allLines = content.split("\n");
                     const body = allLines

package/dist/commands/search-run.js

@@ -42,15 +42,23 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
     });
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.shouldFallbackFromDaemonError = shouldFallbackFromDaemonError;
 exports.runSearch = runSearch;
 const path = __importStar(require("node:path"));
 const config_1 = require("../config");
+const embedding_status_1 = require("../lib/index/embedding-status");
 const grammar_loader_1 = require("../lib/index/grammar-loader");
+const index_config_1 = require("../lib/index/index-config");
 const sync_helpers_1 = require("../lib/index/sync-helpers");
 const syncer_1 = require("../lib/index/syncer");
 const searcher_1 = require("../lib/search/searcher");
 const vector_db_1 = require("../lib/store/vector-db");
 const lock_1 = require("../lib/utils/lock");
+const project_registry_1 = require("../lib/utils/project-registry");
+const DAEMON_FALLBACK_ERRORS = new Set(["ENOENT", "ECONNREFUSED"]);
+function shouldFallbackFromDaemonError(error) {
+    return typeof error === "string" && DAEMON_FALLBACK_ERRORS.has(error);
+}
 /**
  * Acquire search results, picking the path: daemon-mediated first (ships the
  * query over IPC to the already-warm daemon), in-process fallback otherwise
@@ -68,48 +76,65 @@ function runSearch(params) {
         // caller for closing after render, or (b) closed here if indexing throws.
         let openedDb = null;
         try {
+            const selectedRoots = Array.isArray(searchFilters.projectRoots)
+                ? new Set(searchFilters.projectRoots)
+                : new Set([projectRoot]);
+            (0, embedding_status_1.assertEmbeddingSearchCompatible)((0, project_registry_1.listProjects)().filter((project) => selectedRoots.has(project.root)), (0, index_config_1.readGlobalConfig)());
             // Daemon-mediated search: ships query+args over IPC, daemon runs the
             // hybrid+rerank against its already-warm VectorDB and worker pool.
             // Drops cold-start cost (~17s wall, 6GB RAM in the CLI) to <1s. Falls
-            // back to in-process on any failure.
+            // back to in-process only when no daemon socket is available. A live daemon
+            // error (busy, rebuilding, timeout, protocol, scope, store failure) must not
+            // open the shared store concurrently.
             let searchResult = null;
             let precomputedSkeletons;
             let precomputedGraph;
             let indexState;
             if (!options.sync && !options.dryRun) {
                 try {
-                    const { isDaemonRunning, sendDaemonCommand } = yield Promise.resolve().then(() => __importStar(require("../lib/utils/daemon-client")));
-                    if (yield isDaemonRunning()) {
-                        const resp = yield sendDaemonCommand({
-                            cmd: "search",
-                            projectRoot: effectiveRoot,
-                            query: pattern,
-                            limit: parseInt(options.m, 10),
-                            filters: Object.keys(searchFilters).length > 0
-                                ? searchFilters
-                                : undefined,
-                            pathPrefix: pathFilter,
-                            rerank: process.env.GMAX_RERANK === "1",
-                            explain: options.explain,
-                            seeds,
-                            includeSkeletons: options.skeleton,
-                            includeGraph: options.symbol,
-                        }, { timeoutMs: 60000 });
-                        if (resp.ok) {
-                            searchResult = {
-                                data: resp.data,
-                                warnings: resp.warnings,
-                            };
-                            precomputedSkeletons = resp.skeletons;
-                            precomputedGraph = resp.graph;
-                            indexState = resp.indexState;
-                        }
-                        else if (process.env.GMAX_DEBUG === "1") {
-                            console.error(`[search] daemon path unavailable: ${(_a = resp.error) !== null && _a !== void 0 ? _a : "unknown"}`);
-                        }
+                    const { sendDaemonCommand } = yield Promise.resolve().then(() => __importStar(require("../lib/utils/daemon-client")));
+                    const crossProject = Array.isArray(searchFilters.projectRoots);
+                    const resp = yield sendDaemonCommand({
+                        cmd: crossProject ? "search-v2" : "search",
+                        projectRoot: effectiveRoot,
+                        query: pattern,
+                        limit: parseInt(options.m, 10),
+                        filters: Object.keys(searchFilters).length > 0 ? searchFilters : undefined,
+                        pathPrefix: pathFilter,
+                        rerank: process.env.GMAX_RERANK === "1",
+                        explain: options.explain,
+                        seeds,
+                        includeSkeletons: options.skeleton,
+                        includeGraph: options.symbol,
+                    }, { timeoutMs: 60000 });
+                    if (resp.ok) {
+                        searchResult = {
+                            data: resp.data,
+                            warnings: resp.warnings,
+                        };
+                        precomputedSkeletons = resp.skeletons;
+                        precomputedGraph = resp.graph;
+                        indexState = resp.indexState;
+                    }
+                    else if (!shouldFallbackFromDaemonError(resp.error)) {
+                        const detail = typeof resp.hint === "string"
+                            ? `: ${resp.hint}`
+                            : typeof resp.error === "string"
+                                ? `: ${resp.error}`
+                                : "";
+                        throw new Error(`Daemon search failed${detail}`);
+                    }
+                    else if (process.env.GMAX_DEBUG === "1") {
+                        console.error(`[search] daemon path unavailable: ${(_a = resp.error) !== null && _a !== void 0 ? _a : "unknown"}`);
                     }
                 }
                 catch (err) {
+                    const code = err === null || err === void 0 ? void 0 : err.code;
+                    if ((err instanceof Error &&
+                        err.message.startsWith("Daemon search failed")) ||
+                        !shouldFallbackFromDaemonError(code)) {
+                        throw err;
+                    }
                     if (process.env.GMAX_DEBUG === "1") {
                         console.error("[search] daemon attempt threw:", err);
                     }
@@ -176,23 +201,26 @@ function runSearch(params) {
                             return { kind: "dry-run", vectorDb: openedDb };
                         }
                         yield vectorDb.createFTSIndex();
-                        // Update registry after sync
-                        const { readGlobalConfig } = yield Promise.resolve().then(() => __importStar(require("../lib/index/index-config")));
-                        const { registerProject } = yield Promise.resolve().then(() => __importStar(require("../lib/utils/project-registry")));
-                        const gc = readGlobalConfig();
-                        registerProject({
-                            root: projectRoot,
-                            name: path.basename(projectRoot),
-                            vectorDim: gc.vectorDim,
-                            modelTier: gc.modelTier,
-                            embedMode: gc.embedMode,
-                            lastIndexed: new Date().toISOString(),
-                            chunkCount: result.indexed,
-                            status: "indexed",
-                            chunkerVersion: config_1.CONFIG.CHUNKER_VERSION,
-                        });
-                        const failedSuffix = result.failedFiles > 0 ? ` • ${result.failedFiles} failed` : "";
-                        spinner.succeed(`${options.sync ? "Indexing" : "Initial indexing"} complete (${result.processed}/${result.total}) • indexed ${result.indexed}${failedSuffix}`);
+                        if (result.degraded) {
+                            spinner.warn(`Indexing incomplete (${result.processed}/${result.total}) • ${result.scanErrors} scan errors • ${result.failedFiles} failed. Results may be partial.`);
+                        }
+                        else {
+                            const prefix = projectRoot.endsWith("/")
+                                ? projectRoot
+                                : `${projectRoot}/`;
+                            const chunkCount = yield vectorDb.countRowsForPath(prefix);
+                            (0, project_registry_1.stampProjectFullSync)({
+                                root: projectRoot,
+                                name: path.basename(projectRoot),
+                                generation: result.generation,
+                                embedMode: result.embedMode,
+                                chunkCount,
+                                chunkerVersion: config_1.CONFIG.CHUNKER_VERSION,
+                                expectedFingerprint: result.registryExpectation.embeddingFingerprint,
+                                expectedRebuildId: result.registryExpectation.rebuildId,
+                            });
+                            spinner.succeed(`${options.sync ? "Indexing" : "Initial indexing"} complete (${result.processed}/${result.total}) • indexed ${result.indexed}`);
+                        }
                     }
                     catch (e) {
                         spinner.fail("Indexing failed");

package/dist/commands/search-skeletons.js

@@ -44,9 +44,9 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.outputSkeletons = outputSkeletons;
 const fs = __importStar(require("node:fs"));
-const path = __importStar(require("node:path"));
 const skeleton_1 = require("../lib/skeleton");
 const retriever_1 = require("../lib/skeleton/retriever");
+const path_containment_1 = require("../lib/utils/path-containment");
 // Reuse Skeletonizer instance
 let globalSkeletonizer = null;
 function outputSkeletons(results, projectRoot, limit, db, precomputed) {
@@ -77,10 +77,19 @@ function outputSkeletons(results, projectRoot, limit, db, precomputed) {
         const skeletonOpts = { includeSummary: true };
         const skeletonResults = [];
         for (const filePath of filesToProcess) {
-            // Paths from search results are now absolute (centralized index)
-            const absPath = path.isAbsolute(filePath)
-                ? filePath
-                : path.resolve(projectRoot, filePath);
+            let absPath;
+            try {
+                absPath = (0, path_containment_1.resolveContainedFile)(projectRoot, filePath);
+            }
+            catch (_c) {
+                skeletonResults.push({
+                    file: filePath,
+                    skeleton: `// File not readable: ${filePath}`,
+                    tokens: 0,
+                    error: "File not readable",
+                });
+                continue;
+            }
             // 0. Daemon-supplied (preferred — already-warm DB lookup, no cold open)
             const fromDaemon = (_b = precomputed === null || precomputed === void 0 ? void 0 : precomputed[absPath]) !== null && _b !== void 0 ? _b : precomputed === null || precomputed === void 0 ? void 0 : precomputed[filePath];
             if (fromDaemon) {
@@ -104,24 +113,25 @@ function outputSkeletons(results, projectRoot, limit, db, precomputed) {
                 }
             }
             // 2. Fallback to fresh generation
-            yield globalSkeletonizer.init();
-            if (!fs.existsSync(absPath)) {
+            try {
+                yield globalSkeletonizer.init();
+                const content = fs.readFileSync(absPath, "utf-8");
+                const res = yield globalSkeletonizer.skeletonizeFile(absPath, content, skeletonOpts);
+                skeletonResults.push({
+                    file: filePath,
+                    skeleton: res.skeleton,
+                    tokens: res.tokenEstimate,
+                    error: res.error,
+                });
+            }
+            catch (_d) {
                 skeletonResults.push({
                     file: filePath,
-                    skeleton: `// File not found: ${filePath}`,
+                    skeleton: `// File not readable: ${filePath}`,
                     tokens: 0,
-                    error: "File not found",
+                    error: "File not readable",
                 });
-                continue;
             }
-            const content = fs.readFileSync(absPath, "utf-8");
-            const res = yield globalSkeletonizer.skeletonizeFile(absPath, content, skeletonOpts);
-            skeletonResults.push({
-                file: filePath,
-                skeleton: res.skeleton,
-                tokens: res.tokenEstimate,
-                error: res.error,
-            });
         }
         // Since search doesn't support --json explicitly yet, we just print text.
         // But if we ever add it, we have the structure.