@phren/cli 0.1.12 → 0.1.13

package/dist/cli/namespaces.js

@@ -1719,6 +1719,26 @@ export async function handleStoreNamespace(args) {
                     stdio: "pipe",
                     timeout: 30_000,
                 });
+                // Re-apply sparse-checkout after pull on primary store to avoid materializing all files
+                if (store.role === "primary") {
+                    try {
+                        const sparseList = execFileSync("git", ["sparse-checkout", "list"], {
+                            cwd: store.path,
+                            stdio: "pipe",
+                            timeout: 10_000,
+                        }).toString().trim();
+                        if (sparseList) {
+                            execFileSync("git", ["sparse-checkout", "reapply"], {
+                                cwd: store.path,
+                                stdio: "pipe",
+                                timeout: 10_000,
+                            });
+                        }
+                    }
+                    catch {
+                        // sparse-checkout not configured — nothing to reapply
+                    }
+                }
                 console.log(`  ${store.name}: ok`);
             }
             catch (err) {

package/dist/profile-store.js

@@ -310,8 +310,19 @@ export function listProjectCards(phrenPath, profile) {
     const dirs = getProjectDirs(phrenPath, profile).sort((a, b) => path.basename(a).localeCompare(path.basename(b)));
     const cards = dirs.map(buildProjectCard);
     const seen = new Set(dirs.map((d) => path.basename(d)));
-    // Include projects from team stores
+    // Include projects from team stores, filtered by active profile
     try {
+        // Resolve the profile's project allow-list (if any)
+        let profileProjectNames;
+        if (profile) {
+            const profiles = listProfiles(phrenPath);
+            if (profiles.ok) {
+                const active = profiles.data.find((p) => p.name === profile);
+                if (active && active.projects.length > 0) {
+                    profileProjectNames = new Set(active.projects);
+                }
+            }
+        }
         for (const store of getNonPrimaryStores(phrenPath)) {
             if (!fs.existsSync(store.path))
                 continue;
@@ -319,6 +330,8 @@ export function listProjectCards(phrenPath, profile) {
                 const name = path.basename(dir);
                 if (seen.has(name) || name === "global")
                     continue;
+                if (profileProjectNames && !profileProjectNames.has(name))
+                    continue;
                 seen.add(name);
                 cards.push(buildProjectCard(dir));
             }

package/dist/shared/index.js

@@ -30,12 +30,30 @@ async function refreshStoreProjectDirs(phrenPath, profile) {
     try {
         const { getNonPrimaryStores, getStoreProjectDirs } = await import("../store-registry.js");
         const otherStores = getNonPrimaryStores(phrenPath);
-        const dirs = [];
+        let dirs = [];
         for (const store of otherStores) {
             if (!fs.existsSync(store.path))
                 continue;
             dirs.push(...getStoreProjectDirs(store));
         }
+        // Filter by active profile's project list, matching getProjectDirs behavior
+        if (profile) {
+            const profilePath = path.join(phrenPath, "profiles", `${profile}.yaml`);
+            if (fs.existsSync(profilePath)) {
+                try {
+                    const yaml = await import("js-yaml");
+                    const data = yaml.load(fs.readFileSync(profilePath, "utf-8"), { schema: yaml.CORE_SCHEMA });
+                    const projects = data?.projects;
+                    if (Array.isArray(projects)) {
+                        const allowed = new Set(projects.map(String));
+                        dirs = dirs.filter(dir => allowed.has(path.basename(dir)));
+                    }
+                }
+                catch {
+                    // Profile parse error — include all dirs as fallback
+                }
+            }
+        }
         _cachedStoreProjectDirs = dirs;
         _cachedStorePhrenPath = phrenPath;
     }
@@ -445,8 +463,9 @@ function globAllFiles(phrenPath, profile) {
     const allAbsolutePaths = [];
     for (const dir of projectDirs) {
         const projectName = path.basename(dir);
-        const config = readProjectConfig(phrenPath, projectName);
-        const ownership = getProjectOwnershipMode(phrenPath, projectName, config);
+        const storePath = path.dirname(dir);
+        const config = readProjectConfig(storePath, projectName);
+        const ownership = getProjectOwnershipMode(storePath, projectName, config);
         const mdFilesSet = new Set();
         for (const pattern of indexPolicy.includeGlobs) {
             const dot = indexPolicy.includeHidden || pattern.startsWith(".") || pattern.includes("/.");

package/dist/shared/retrieval.js

@@ -495,20 +495,21 @@ export async function searchKnowledgeRows(db, options) {
  * Returns an array of results tagged with their source store. Read-only — no mutations.
  */
 export async function searchFederatedStores(localPhrenPath, options) {
-    let nonPrimaryStores;
+    // Registered non-primary stores are already included in the main FTS index
+    // by buildIndex (via refreshStoreProjectDirs). Only search unregistered
+    // federation paths from PHREN_FEDERATION_PATHS to avoid double indexing.
+    let registeredStorePaths;
     try {
         const { getNonPrimaryStores } = await import("../store-registry.js");
-        nonPrimaryStores = getNonPrimaryStores(localPhrenPath).map((s) => ({
-            path: s.path, name: s.name, id: s.id,
-        }));
+        registeredStorePaths = new Set(getNonPrimaryStores(localPhrenPath).map((s) => s.path));
     }
     catch {
-        // Fallback: parse PHREN_FEDERATION_PATHS directly (pre-registry compat)
-        const raw = process.env.PHREN_FEDERATION_PATHS ?? "";
-        nonPrimaryStores = raw.split(":").map((p) => p.trim())
-            .filter((p) => p.length > 0 && p !== localPhrenPath && fs.existsSync(p))
-            .map((p) => ({ path: p, name: path.basename(p), id: "" }));
+        registeredStorePaths = new Set();
     }
+    const raw = process.env.PHREN_FEDERATION_PATHS ?? "";
+    const nonPrimaryStores = raw.split(":").map((p) => p.trim())
+        .filter((p) => p.length > 0 && p !== localPhrenPath && !registeredStorePaths.has(p) && fs.existsSync(p))
+        .map((p) => ({ path: p, name: path.basename(p), id: "" }));
     if (nonPrimaryStores.length === 0)
         return [];
     const allRows = [];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.1.12",
+  "version": "0.1.13",
   "description": "Knowledge layer for AI agents — CLI, MCP server, and data layer",
   "type": "module",
   "bin": {