@phren/cli 0.0.34 → 0.0.36

package/mcp/dist/data/access.js

@@ -113,6 +113,7 @@ export function readFindings(phrenPath, project, opts = {}) {
     let date = "unknown";
     let index = 1;
     let inArchiveBlock = false;
+    let headingTag;
     const includeArchived = opts.includeArchived ?? false;
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i];
@@ -134,6 +135,39 @@ export function readFindings(phrenPath, project, opts = {}) {
             date = extractedDate;
             continue;
         }
+        // Support heading-based findings: ## topic / ### title / paragraph
+        const h2TagMatch = line.match(/^##\s+([a-z_-]+)\s*$/i);
+        if (h2TagMatch && !line.match(/^##\s+\d{4}/)) {
+            // Track topic heading (but not date headings like ## 2026-03-22)
+            headingTag = h2TagMatch[1].toLowerCase();
+            continue;
+        }
+        const h3Match = line.match(/^###\s+(.+)$/);
+        if (h3Match && headingTag) {
+            let body = "";
+            for (let j = i + 1; j < lines.length; j++) {
+                const next = lines[j].trim();
+                if (!next)
+                    continue;
+                if (next.startsWith("#") || next.startsWith("- "))
+                    break;
+                body = next;
+                break;
+            }
+            const title = h3Match[1].trim();
+            const syntheticText = body ? `[${headingTag}] ${title} — ${body}` : `[${headingTag}] ${title}`;
+            items.push({
+                id: `L${index}`,
+                date,
+                text: syntheticText,
+                source: "unknown",
+                status: "active",
+                archived: inArchiveBlock,
+                tier: inArchiveBlock ? "archived" : "current",
+            });
+            index++;
+            continue;
+        }
         if (!line.startsWith("- "))
             continue;
         const next = lines[i + 1] || "";

package/mcp/dist/hooks.js

@@ -218,12 +218,15 @@ export function installPhrenCliWrapper(phrenPath) {
             if (!existing.includes("PHREN_CLI_WRAPPER"))
                 return false;
         }
-        catch { /* unreadable — skip */ }
+        catch {
+            // File exists but unreadable — don't overwrite, could be a real binary
+            return false;
+        }
     }
     const content = `#!/bin/sh
 # PHREN_CLI_WRAPPER — managed by phren init; safe to delete
 set -u
-PHREN_PATH="\${PHREN_PATH:-${shellEscape(phrenPath)}}"
+PHREN_PATH="\${PHREN_PATH:-${phrenPath}}"
 export PHREN_PATH
 exec node ${shellEscape(entry)} "$@"
 `;

package/mcp/dist/init/init.js

@@ -118,7 +118,7 @@ export function parseMcpMode(raw) {
 function normalizedBootstrapProjectName(projectPath) {
     return path.basename(projectPath).toLowerCase().replace(/[^a-z0-9_-]/g, "-");
 }
-function getPendingBootstrapTarget(phrenPath, opts) {
+function getPendingBootstrapTarget(phrenPath, _opts) {
     const cwdProject = detectProjectDir(process.cwd(), phrenPath);
     if (!cwdProject)
         return null;
@@ -970,13 +970,12 @@ function configureHooksIfEnabled(phrenPath, hooksEnabled, verb) {
         log(`  Hooks are disabled by preference (run: npx phren hooks-mode on)`);
     }
     // Install phren CLI wrapper at ~/.local/bin/phren so the bare command works
-    try {
-        if (installPhrenCliWrapper(phrenPath)) {
-            log(`  ${verb} CLI wrapper: ~/.local/bin/phren`);
-        }
+    const wrapperInstalled = installPhrenCliWrapper(phrenPath);
+    if (wrapperInstalled) {
+        log(`  ${verb} CLI wrapper: ~/.local/bin/phren`);
     }
-    catch (err) {
-        debugLog(`installPhrenCliWrapper failed: ${errorMessage(err)}`);
+    else {
+        log(`  Note: phren CLI wrapper not installed (existing non-managed binary, or no entry script found)`);
     }
 }
 export async function runInit(opts = {}) {

package/mcp/dist/init/setup.js

@@ -6,6 +6,7 @@ import * as path from "path";
 import * as os from "os";
 import * as yaml from "js-yaml";
 import { atomicWriteText, debugLog, findProjectNameCaseInsensitive, hookConfigPath, EXEC_TIMEOUT_QUICK_MS, readRootManifest, sessionsDir, runtimeHealthFile, isRecord, } from "../shared.js";
+import { homePath } from "../phren-paths.js";
 import { addProjectToProfile, listProfiles, resolveActiveProfile, setMachineProfile } from "../profile-store.js";
 import { getMachineName } from "../machine-identity.js";
 import { execFileSync } from "child_process";
@@ -1271,6 +1272,25 @@ export function runPostInitVerify(phrenPath) {
         fix: ftsOk ? undefined : "Create a project: `cd ~/your-project && phren add`",
     });
     checks.push(getHookEntrypointCheck());
+    // Check that the CLI wrapper at ~/.local/bin/phren exists and is executable (soft check — not mandatory)
+    const cliWrapperPath = homePath(".local", "bin", "phren");
+    let cliWrapperOk = false;
+    try {
+        const stat = fs.statSync(cliWrapperPath);
+        cliWrapperOk = stat.isFile();
+        if (cliWrapperOk)
+            fs.accessSync(cliWrapperPath, fs.constants.X_OK);
+    }
+    catch {
+        cliWrapperOk = false;
+    }
+    checks.push({
+        name: "cli-wrapper",
+        ok: true, // always pass — wrapper is optional (global install or npx work too)
+        detail: cliWrapperOk
+            ? `CLI wrapper exists: ${cliWrapperPath}`
+            : `CLI wrapper not found (optional — use 'npm i -g @phren/cli' or 'npx @phren/cli' instead)`,
+    });
     const ok = checks.every((c) => c.ok);
     return { ok, checks };
 }

package/mcp/dist/shared/fragment-graph.js

@@ -232,7 +232,7 @@ function parseUserDefinedFragments(phrenPath, project) {
     }
 }
 /** Clear the user fragment cache (call between index builds). */
-function clearUserFragmentCache() {
+function _clearUserFragmentCache() {
     _userFragmentCache.clear();
     _buildUserFragmentCache.clear();
     _activeBuildCacheKeyPrefix = null;

package/mcp/dist/shell/entry.js

@@ -63,7 +63,7 @@ async function playStartupIntro(phrenPath, plan = resolveStartupIntroPlan(phrenP
     // Start animated phren during loading
     const animator = createPhrenAnimator({ facing: "right" });
     animator.start();
-    const cols = process.stdout.columns || 80;
+    const _cols = process.stdout.columns || 80;
     const tagline = style.dim("local memory for working agents");
     const versionBadge = badge(`v${VERSION}`, style.boldBlue);
     const logoLines = [

package/mcp/dist/tools/search.js

@@ -456,7 +456,6 @@ async function handleSearchKnowledge(ctx, { query, limit, project, type, tag, si
     }
 }
 async function handleGetProjectSummary(ctx, { name }) {
-    const { phrenPath } = ctx;
     const db = ctx.db();
     const docs = queryDocRows(db, "SELECT project, filename, type, content, path FROM docs WHERE project = ?", [name]);
     if (!docs) {

package/mcp/dist/ui/data.js

@@ -194,8 +194,62 @@ export async function buildGraph(phrenPath, profile, focusProject, existingDb) {
         const MAX_UNTAGGED = isFocused ? Infinity : 100;
         let taggedCount = 0;
         let untaggedAdded = 0;
-        for (const line of lines) {
-            // Support legacy tagged findings like [decision], [pitfall], etc.
+        // Support heading-based findings: ## topic / ### title / paragraph
+        let currentHeadingTag;
+        let _currentHeadingTitle;
+        for (let lineIdx = 0; lineIdx < lines.length; lineIdx++) {
+            const line = lines[lineIdx];
+            // Track heading context for heading-based findings
+            const h2Match = line.match(/^##\s+([a-z_-]+)\s*$/i);
+            if (h2Match) {
+                currentHeadingTag = h2Match[1].toLowerCase();
+                _currentHeadingTitle = undefined;
+                continue;
+            }
+            const h3Match = line.match(/^###\s+(.+)$/);
+            if (h3Match && currentHeadingTag) {
+                // Read the next non-empty line as the body
+                let body = "";
+                for (let j = lineIdx + 1; j < lines.length; j++) {
+                    const next = lines[j].trim();
+                    if (!next)
+                        continue;
+                    if (next.startsWith("#"))
+                        break;
+                    body = next;
+                    break;
+                }
+                const title = h3Match[1].trim();
+                const text = body ? `${title} — ${body}` : title;
+                if (text.length >= 10) {
+                    if (taggedCount >= MAX_TAGGED)
+                        continue;
+                    const topic = classifyTopicForText(`[${currentHeadingTag}] ${text}`, projectTopics);
+                    const scoreKey = entryScoreKey(project, "FINDINGS.md", `[${currentHeadingTag}] ${text}`);
+                    const nodeId = stableId("finding", scoreKey);
+                    taggedCount++;
+                    nodes.push({
+                        id: nodeId,
+                        label: text.length > 55 ? `${text.slice(0, 52)}...` : text,
+                        fullLabel: text,
+                        group: `topic:${topic.slug}`,
+                        refCount: taggedCount,
+                        project,
+                        tagged: true,
+                        scoreKey,
+                        scoreKeys: [scoreKey],
+                        refDocs: [{ doc: `${project}/FINDINGS.md`, project, scoreKey }],
+                        topicSlug: topic.slug,
+                        topicLabel: topic.label,
+                    });
+                    links.push({ source: project, target: nodeId });
+                    for (const other of exactProjectMentions(text, projectSet, project)) {
+                        links.push({ source: project, target: other });
+                    }
+                }
+                continue;
+            }
+            // Standard bullet-based findings: - [tag] text
             const tagMatch = line.match(/^-\s+\[([a-z_-]+)\]\s+(.+?)(?:\s*<!--.*-->)?$/);
             if (tagMatch) {
                 if (taggedCount >= MAX_TAGGED)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.0.34",
+  "version": "0.0.36",
   "description": "Knowledge layer for AI agents. Phren learns and recalls.",
   "type": "module",
   "bin": {