@phren/cli 0.0.52 → 0.0.54

package/mcp/dist/profile-store.js

@@ -8,6 +8,7 @@ import { errorMessage, isValidProjectName } from "./utils.js";
 import { TASK_FILE_ALIASES } from "./data/tasks.js";
 import { withSafeLock } from "./shared/data-utils.js";
 import { logger } from "./logger.js";
+import { getNonPrimaryStores, getStoreProjectDirs } from "./store-registry.js";
 export function resolveActiveProfile(phrenPath, requestedProfile) {
     const manifest = readRootManifest(phrenPath);
     if (manifest?.installMode === "project-local") {
@@ -308,12 +309,10 @@ export function listProjectCards(phrenPath, profile) {
     const seen = new Set(dirs.map((d) => path.basename(d)));
     // Include projects from team stores
     try {
-        const storeRegistry = require("./store-registry.js");
-        const { getNonPrimaryStores } = storeRegistry;
         for (const store of getNonPrimaryStores(phrenPath)) {
             if (!fs.existsSync(store.path))
                 continue;
-            for (const dir of getProjectDirs(store.path)) {
+            for (const dir of getStoreProjectDirs(store)) {
                 const name = path.basename(dir);
                 if (seen.has(name) || name === "global")
                     continue;

package/mcp/dist/shared/index.js

@@ -28,13 +28,13 @@ function getAllStoreProjectDirs(phrenPath, profile) {
  */
 async function refreshStoreProjectDirs(phrenPath, profile) {
     try {
-        const { getNonPrimaryStores } = await import("../store-registry.js");
+        const { getNonPrimaryStores, getStoreProjectDirs } = await import("../store-registry.js");
         const otherStores = getNonPrimaryStores(phrenPath);
         const dirs = [];
         for (const store of otherStores) {
             if (!fs.existsSync(store.path))
                 continue;
-            dirs.push(...getProjectDirs(store.path));
+            dirs.push(...getStoreProjectDirs(store));
         }
         _cachedStoreProjectDirs = dirs;
         _cachedStorePhrenPath = phrenPath;

package/mcp/dist/shell/view.js

@@ -457,7 +457,8 @@ function renderMemoryQueueView(ctx, cursor, height) {
     return vp.lines;
 }
 export function getProjectSkills(phrenPath, project) {
-    return getScopedSkills(phrenPath, "", project).map((skill) => ({
+    const storePath = resolveProjectStorePath(phrenPath, project);
+    return getScopedSkills(storePath, "", project).map((skill) => ({
         name: skill.name,
         path: skill.path,
         enabled: skill.enabled,
@@ -541,10 +542,11 @@ const LIFECYCLE_HOOKS = [
 export function getHookEntries(phrenPath, project) {
     const prefs = readInstallPreferences(phrenPath);
     const hooksEnabled = prefs.hooksEnabled !== false;
-    const projectConfig = project ? readProjectConfig(phrenPath, project) : undefined;
+    const storePath = project ? resolveProjectStorePath(phrenPath, project) : phrenPath;
+    const projectConfig = project ? readProjectConfig(storePath, project) : undefined;
     return LIFECYCLE_HOOKS.map((h) => ({
         ...h,
-        enabled: hooksEnabled && isProjectHookEnabled(phrenPath, project, h.event, projectConfig),
+        enabled: hooksEnabled && isProjectHookEnabled(storePath, project, h.event, projectConfig),
     }));
 }
 function renderHooksView(ctx, cursor, height) {

package/mcp/dist/store-registry.js

@@ -5,6 +5,7 @@ import * as yaml from "js-yaml";
 import { expandHomePath, atomicWriteText } from "./phren-paths.js";
 import { withFileLock } from "./governance/locks.js";
 import { isRecord, PhrenError } from "./phren-core.js";
+import { getProjectDirs } from "./shared.js";
 // ── Constants ────────────────────────────────────────────────────────────────
 const STORES_FILENAME = "stores.yaml";
 const TEAM_BOOTSTRAP_FILENAME = ".phren-team.yaml";
@@ -110,6 +111,14 @@ export function getNonPrimaryStores(phrenPath) {
 export function findStoreByName(phrenPath, name) {
     return resolveAllStores(phrenPath).find((s) => s.name === name);
 }
+/** Get project directories for a store, filtered by the store's subscription list (if set). */
+export function getStoreProjectDirs(store) {
+    const allDirs = getProjectDirs(store.path);
+    if (!store.projects || store.projects.length === 0)
+        return allDirs;
+    const allowed = new Set(store.projects);
+    return allDirs.filter(dir => path.basename(dir) !== "global" && allowed.has(path.basename(dir)));
+}
 // ── Team bootstrap ───────────────────────────────────────────────────────────
 export function readTeamBootstrap(storePath) {
     const filePath = path.join(storePath, TEAM_BOOTSTRAP_FILENAME);
@@ -178,6 +187,38 @@ export function updateStoreProjects(phrenPath, storeName, projects) {
         writeStoreRegistry(phrenPath, registry);
     });
 }
+/** Add projects to a store's subscription list. Deduplicates. Uses file locking. */
+export function subscribeStoreProjects(phrenPath, storeName, projects) {
+    withFileLock(storesFilePath(phrenPath), () => {
+        const registry = readStoreRegistry(phrenPath);
+        if (!registry)
+            throw new Error(`${PhrenError.FILE_NOT_FOUND}: No stores.yaml found`);
+        const store = registry.stores.find((s) => s.name === storeName);
+        if (!store)
+            throw new Error(`${PhrenError.NOT_FOUND}: Store "${storeName}" not found`);
+        const existing = new Set(store.projects || []);
+        for (const project of projects) {
+            existing.add(project);
+        }
+        store.projects = Array.from(existing).sort().length > 0 ? Array.from(existing).sort() : undefined;
+        writeStoreRegistry(phrenPath, registry);
+    });
+}
+/** Remove projects from a store's subscription list. Uses file locking. */
+export function unsubscribeStoreProjects(phrenPath, storeName, projects) {
+    withFileLock(storesFilePath(phrenPath), () => {
+        const registry = readStoreRegistry(phrenPath);
+        if (!registry)
+            throw new Error(`${PhrenError.FILE_NOT_FOUND}: No stores.yaml found`);
+        const store = registry.stores.find((s) => s.name === storeName);
+        if (!store)
+            throw new Error(`${PhrenError.NOT_FOUND}: Store "${storeName}" not found`);
+        const toRemove = new Set(projects);
+        const remaining = (store.projects || []).filter((p) => !toRemove.has(p));
+        store.projects = remaining.length > 0 ? remaining : undefined;
+        writeStoreRegistry(phrenPath, registry);
+    });
+}
 // ── Validation ───────────────────────────────────────────────────────────────
 function validateRegistry(registry) {
     if (registry.version !== 1)

package/mcp/dist/tools/data.js

@@ -282,15 +282,16 @@ export function register(server, ctx) {
     }, async ({ project, action }) => {
         if (!isValidProjectName(project))
             return mcpResponse({ ok: false, error: `Invalid project name: "${project}"` });
+        const resolved = resolveStoreForProject(ctx, project);
         return withWriteQueue(async () => {
-            const activeProject = findProjectNameCaseInsensitive(phrenPath, project);
-            const archivedProject = findArchivedProjectNameCaseInsensitive(phrenPath, project);
+            const activeProject = findProjectNameCaseInsensitive(resolved.phrenPath, project);
+            const archivedProject = findArchivedProjectNameCaseInsensitive(resolved.phrenPath, project);
             if (action === "archive") {
                 if (!activeProject) {
                     return mcpResponse({ ok: false, error: `Project "${project}" not found.` });
                 }
-                const projectDir = path.join(phrenPath, activeProject);
-                const archiveDir = path.join(phrenPath, `${activeProject}.archived`);
+                const projectDir = path.join(resolved.phrenPath, activeProject);
+                const archiveDir = path.join(resolved.phrenPath, `${activeProject}.archived`);
                 if (!fs.existsSync(projectDir)) {
                     return mcpResponse({ ok: false, error: `Project "${project}" not found.` });
                 }
@@ -316,12 +317,12 @@ export function register(server, ctx) {
                 return mcpResponse({ ok: false, error: `Project "${activeProject}" already exists as an active project.` });
             }
             if (!archivedProject) {
-                const entries = fs.readdirSync(phrenPath).filter((e) => e.endsWith(".archived"));
+                const entries = fs.readdirSync(resolved.phrenPath).filter((e) => e.endsWith(".archived"));
                 const available = entries.map((e) => e.replace(/\.archived$/, ""));
                 return mcpResponse({ ok: false, error: `No archive found for "${project}".`, data: { availableArchives: available } });
             }
-            const projectDir = path.join(phrenPath, archivedProject);
-            const archiveDir = path.join(phrenPath, `${archivedProject}.archived`);
+            const projectDir = path.join(resolved.phrenPath, archivedProject);
+            const archiveDir = path.join(resolved.phrenPath, `${archivedProject}.archived`);
             fs.renameSync(archiveDir, projectDir);
             try {
                 await rebuildIndex();

package/mcp/dist/tools/search.js

@@ -3,6 +3,7 @@ import { z } from "zod";
 import * as fs from "fs";
 import * as path from "path";
 import { createHash } from "crypto";
+import { execFileSync } from "child_process";
 import { isValidProjectName, errorMessage } from "../utils.js";
 import { resolveAllStores } from "../store-registry.js";
 import { readFindings } from "../data/access.js";
@@ -529,14 +530,13 @@ async function handleListProjects(ctx, { page, page_size }) {
         ? projectRows.map(row => decodeStringRow(row, 1, "list_projects.projects")[0])
         : [];
     // Gather projects from non-primary stores
-    const { getNonPrimaryStores } = await import("../store-registry.js");
-    const { getProjectDirs } = await import("../phren-paths.js");
+    const { getNonPrimaryStores, getStoreProjectDirs } = await import("../store-registry.js");
     const nonPrimaryStores = getNonPrimaryStores(phrenPath);
     const storeProjects = [];
     for (const store of nonPrimaryStores) {
         if (!fs.existsSync(store.path))
             continue;
-        const dirs = getProjectDirs(store.path);
+        const dirs = getStoreProjectDirs(store);
         for (const dir of dirs) {
             const projName = path.basename(dir);
             storeProjects.push({ name: projName, store: store.name });
@@ -691,12 +691,11 @@ async function handleStoreList(ctx) {
     const { phrenPath } = ctx;
     const stores = resolveAllStores(phrenPath);
     const storeData = stores.map((store) => {
-        let health = null;
+        // Get last sync time from git log
+        let lastSync = null;
         try {
-            const healthPath = path.join(store.path, ".runtime", "health.json");
-            if (fs.existsSync(healthPath)) {
-                health = JSON.parse(fs.readFileSync(healthPath, "utf8"))?.lastSync ?? null;
-            }
+            const result = execFileSync("git", ["log", "-1", "--format=%ci"], { cwd: store.path, encoding: "utf8", timeout: 3000 }).trim();
+            lastSync = result || null;
         }
         catch { /* non-critical */ }
         return {
@@ -708,7 +707,7 @@ async function handleStoreList(ctx) {
             remote: store.remote ?? null,
             exists: fs.existsSync(store.path),
             projects: store.projects ?? null,
-            lastSync: health,
+            lastSync,
         };
     });
     const lines = storeData.map((s) => {

package/mcp/dist/tools/session.js

@@ -355,11 +355,11 @@ export async function getSessionArtifacts(phrenPath, sessionId, project) {
         }
         // Team store projects
         try {
-            const { getNonPrimaryStores } = await import("../store-registry.js");
+            const { getNonPrimaryStores, getStoreProjectDirs } = await import("../store-registry.js");
             for (const store of getNonPrimaryStores(phrenPath)) {
                 if (!fs.existsSync(store.path))
                     continue;
-                const storeDirs = getProjectDirs(store.path).map(d => path.basename(d)).filter(p => p !== "global");
+                const storeDirs = getStoreProjectDirs(store).map((d) => path.basename(d)).filter((p) => p !== "global");
                 const storeTargetProjects = project ? (storeDirs.includes(project) ? [project] : []) : storeDirs;
                 for (const proj of storeTargetProjects) {
                     readProjectArtifacts(store.path, proj);

package/mcp/dist/ui/data.js

@@ -2,7 +2,7 @@ import * as fs from "fs";
 import * as path from "path";
 import { createHash } from "crypto";
 import { getProjectDirs, runtimeDir, runtimeHealthFile, memoryUsageLogFile, homePath, } from "../shared.js";
-import { getNonPrimaryStores } from "../store-registry.js";
+import { getNonPrimaryStores, getStoreProjectDirs } from "../store-registry.js";
 import { errorMessage } from "../utils.js";
 import { readInstallPreferences } from "../init/preferences.js";
 import { readCustomHooks } from "../hooks.js";
@@ -158,11 +158,15 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
         .filter((project) => project !== "global");
     for (const project of primaryProjects)
         storeProjects.push({ storePath: phrenPath, project });
+    // Map store paths to store names
+    const storePathToName = new Map();
+    storePathToName.set(phrenPath, "primary");
     for (const store of getNonPrimaryStores(phrenPath)) {
         if (!fs.existsSync(store.path))
             continue;
+        storePathToName.set(store.path, store.name);
         try {
-            const storeProjectDirs = getProjectDirs(store.path)
+            const storeProjectDirs = getStoreProjectDirs(store)
                 .map((projectDir) => path.basename(projectDir))
                 .filter((project) => project !== "global");
             for (const project of storeProjectDirs)
@@ -187,6 +191,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
             }
         }
         const findingsPath = path.join(storePath, project, "FINDINGS.md");
+        const storeName = storePathToName.get(storePath) || "unknown";
         if (!fs.existsSync(findingsPath)) {
             if (!addedProjectNodeIds.has(project)) {
                 addedProjectNodeIds.add(project);
@@ -197,6 +202,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                     group: "project",
                     refCount: 0,
                     project,
+                    store: storeName,
                     tagged: false,
                 });
             }
@@ -211,6 +217,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                 group: "project",
                 refCount: 1,
                 project,
+                store: storeName,
                 tagged: false,
             });
         }
@@ -263,6 +270,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                         group: `topic:${topic.slug}`,
                         refCount: taggedCount,
                         project,
+                        store: storeName,
                         tagged: true,
                         scoreKey,
                         scoreKeys: [scoreKey],
@@ -297,6 +305,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                     group: `topic:${topic.slug}`,
                     refCount: taggedCount,
                     project,
+                    store: storeName,
                     tagged: true,
                     scoreKey,
                     scoreKeys: [scoreKey],
@@ -331,6 +340,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                 group: `topic:${topic.slug}`,
                 refCount: untaggedAdded,
                 project,
+                store: storeName,
                 tagged: false,
                 scoreKey,
                 scoreKeys: [scoreKey],
@@ -347,6 +357,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
             const taskResult = readTasks(storePath, project);
             if (!taskResult.ok)
                 continue;
+            const taskStoreName = storePathToName.get(storePath) || "unknown";
             const doc = taskResult.data;
             let taskCount = 0;
             const MAX_TASKS = 50;
@@ -364,6 +375,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                         fullLabel: item.line,
                         group,
                         project,
+                        store: taskStoreName,
                         tagged: false,
                         scoreKey,
                         scoreKeys: [scoreKey],
@@ -431,6 +443,14 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                     .map((ref) => ref.scoreKey)
                     .filter((key) => Boolean(key))
                     .sort();
+                // Only include entities that link to at least one visible project
+                const linkedProjects = new Set();
+                for (const ref of refs) {
+                    if (ref.project && projectSet.has(ref.project))
+                        linkedProjects.add(ref.project);
+                }
+                if (linkedProjects.size === 0)
+                    continue; // skip orphan entities from other profiles/stores
                 const nodeId = `entity:${stableId("entity", type, name)}`;
                 nodes.push({
                     id: nodeId,
@@ -445,12 +465,6 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                     entityType: type,
                     refDocs: refs,
                 });
-                // Link fragment to each project it appears in
-                const linkedProjects = new Set();
-                for (const ref of refs) {
-                    if (ref.project && projectSet.has(ref.project))
-                        linkedProjects.add(ref.project);
-                }
                 for (const proj of linkedProjects) {
                     links.push({ source: nodeId, target: proj });
                 }
@@ -471,6 +485,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
     // ── Reference docs ────────────────────────────────────────────────
     try {
         for (const { storePath, project } of storeProjects) {
+            const refStoreName = storePathToName.get(storePath) || "unknown";
             const refDir = path.join(storePath, project, "reference");
             if (!fs.existsSync(refDir) || !fs.statSync(refDir).isDirectory())
                 continue;
@@ -488,6 +503,7 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
                     fullLabel: file,
                     group: "reference",
                     project,
+                    store: refStoreName,
                     tagged: false,
                     scoreKeys: [],
                     refDocs: [{ doc: docRef, project }],
@@ -640,7 +656,7 @@ export function collectProjectsForUI(phrenPath, profile) {
         for (const store of teamStores) {
             if (!fs.existsSync(store.path))
                 continue;
-            const teamProjects = getProjectDirs(store.path).map((d) => path.basename(d)).filter((p) => p !== "global");
+            const teamProjects = getStoreProjectDirs(store).map((d) => path.basename(d)).filter((p) => p !== "global");
             for (const project of teamProjects) {
                 if (seen.has(project))
                     continue; // skip if same name exists in primary

package/mcp/dist/ui/page.js

@@ -203,6 +203,7 @@ ${REVIEW_UI_STYLES}
         <button id="graph-zoom-in" title="Zoom in">+</button>
         <button id="graph-zoom-out" title="Zoom out">-</button>
         <button id="graph-reset" title="Reset view">R</button>
+        <button id="graph-reset-layout" title="Re-run layout">L</button>
       </div>
       <div class="graph-filters">
         <div class="graph-filter" id="graph-filter"></div>

package/mcp/dist/ui/scripts.js

@@ -1466,6 +1466,8 @@ export function renderEventWiringScript() {
   if (graphZoomOut) graphZoomOut.addEventListener('click', function() { graphZoom(0.8); });
   var graphResetBtn = document.getElementById('graph-reset');
   if (graphResetBtn) graphResetBtn.addEventListener('click', function() { graphReset(); });
+  var graphResetLayoutBtn = document.getElementById('graph-reset-layout');
+  if (graphResetLayoutBtn) graphResetLayoutBtn.addEventListener('click', function() { if (typeof graphResetLayout === 'function') graphResetLayout(); });
 
   // --- Tasks filters ---
   var tasksFilterProject = document.getElementById('tasks-filter-project');

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.0.52",
+  "version": "0.0.54",
   "description": "Knowledge layer for AI agents. Phren learns and recalls.",
   "type": "module",
   "bin": {