@phren/cli 0.0.32 → 0.0.33

package/mcp/dist/content/learning.js

@@ -123,7 +123,8 @@ export function autoDetectFindingType(text) {
         return 'context';
     return null;
 }
-function prepareFinding(learning, project, fullHistory, extraAnnotations, citationInput, source, nowIso, inferredRepo, headCommit, phrenPath) {
+function prepareFinding(opts) {
+    const { finding: learning, project, fullHistory, extraAnnotations, citationInput, source, nowIso, inferredRepo, headCommit, phrenPath } = opts;
     const secretType = scanForSecrets(learning);
     if (secretType) {
         return { status: "rejected", reason: `Contains ${secretType}` };
@@ -208,7 +209,11 @@ function insertFindingIntoContent(content, today, bullet, citationComment) {
     // Use positional insertion (not String.replace) to avoid: (1) special $& replacement patterns
     // if bullet contains $ chars, and (2) inserting inside an archived <details> block when a
     // duplicate date header exists from a prior consolidation run.
-    const idx = content.indexOf(todayHeader);
+    // Search for todayHeader only after the last </details> close tag so we never
+    // insert into an archived block whose date happens to match today.
+    const lastDetailsClose = content.lastIndexOf("</details>");
+    const searchFrom = lastDetailsClose >= 0 ? lastDetailsClose : 0;
+    const idx = content.indexOf(todayHeader, searchFrom);
     if (idx !== -1) {
         const insertAt = idx + todayHeader.length;
         return content.slice(0, insertAt) + `\n\n${bullet}\n${citationComment}` + content.slice(insertAt);
@@ -288,7 +293,10 @@ export function addFindingToFile(phrenPath, project, learning, citationInput, op
     if (!fs.existsSync(resolvedDir))
         return phrenErr(`Project "${project}" does not exist.`, PhrenError.INVALID_PROJECT_NAME);
     const result = withFileLock(learningsPath, () => {
-        const preparedForNewFile = prepareFinding(learning, project, "", opts?.extraAnnotations, resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath);
+        const preparedForNewFile = prepareFinding({
+            finding: learning, project, fullHistory: "", extraAnnotations: opts?.extraAnnotations,
+            citationInput: resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath,
+        });
         if (!fs.existsSync(learningsPath)) {
             if (preparedForNewFile.status === "rejected") {
                 return phrenErr(`Rejected: finding appears to contain a secret (${preparedForNewFile.reason.replace(/^Contains /, "")}). Strip credentials before saving.`, PhrenError.VALIDATION_ERROR);
@@ -297,7 +305,9 @@ export function addFindingToFile(phrenPath, project, learning, citationInput, op
                 return phrenOk(`Skipped duplicate finding for "${project}": already exists with similar wording.`);
             }
             const newContent = `# ${project} Findings\n\n## ${today}\n\n${preparedForNewFile.finding.bullet}\n${preparedForNewFile.finding.citationComment}\n`;
-            fs.writeFileSync(learningsPath, newContent);
+            const tmpPath = learningsPath + ".tmp." + process.pid;
+            fs.writeFileSync(tmpPath, newContent);
+            fs.renameSync(tmpPath, learningsPath);
             return phrenOk({
                 content: newContent,
                 citation: buildFindingCitation(resolvedCitationInput, nowIso, inferredRepo, headCommit),
@@ -316,7 +326,10 @@ export function addFindingToFile(phrenPath, project, learning, citationInput, op
                 .filter(line => !line.startsWith("- ") || !line.toLowerCase().includes(supersedesText.slice(0, 40).toLowerCase()))
                 .join("\n")
             : content;
-        const prepared = prepareFinding(learning, project, historyForDedup, opts?.extraAnnotations, resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath);
+        const prepared = prepareFinding({
+            finding: learning, project, fullHistory: historyForDedup, extraAnnotations: opts?.extraAnnotations,
+            citationInput: resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath,
+        });
         if (prepared.status === "rejected") {
             return phrenErr(`Rejected: finding appears to contain a secret (${prepared.reason.replace(/^Contains /, "")}). Strip credentials before saving.`, PhrenError.VALIDATION_ERROR);
         }
@@ -430,7 +443,10 @@ export function addFindingsToFile(phrenPath, project, learnings, opts) {
                     rejected.push({ text: learning, reason: lengthError });
                     continue;
                 }
-                const prepared = prepareFinding(learning, project, content, extraAnnotations, resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath);
+                const prepared = prepareFinding({
+                    finding: learning, project, fullHistory: content, extraAnnotations,
+                    citationInput: resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath,
+                });
                 if (prepared.status === "rejected") {
                     rejected.push({ text: learning, reason: prepared.reason });
                     continue;
@@ -445,7 +461,9 @@ export function addFindingsToFile(phrenPath, project, learnings, opts) {
                 added.push(learning);
             }
             if (added.length > 0) {
-                fs.writeFileSync(learningsPath, content.endsWith("\n") ? content : `${content}\n`);
+                const tmpPath = learningsPath + ".tmp." + process.pid;
+                fs.writeFileSync(tmpPath, content.endsWith("\n") ? content : `${content}\n`);
+                fs.renameSync(tmpPath, learningsPath);
             }
             return phrenOk({ content, wrote: added.length > 0 });
         }
@@ -460,7 +478,10 @@ export function addFindingsToFile(phrenPath, project, learnings, opts) {
                 rejected.push({ text: learning, reason: lengthError });
                 continue;
             }
-            const prepared = prepareFinding(learning, project, content, extraAnnotations, resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath);
+            const prepared = prepareFinding({
+                finding: learning, project, fullHistory: content, extraAnnotations,
+                citationInput: resolvedCitationInput, source, nowIso, inferredRepo, headCommit, phrenPath,
+            });
             if (prepared.status === "rejected") {
                 rejected.push({ text: learning, reason: prepared.reason });
                 continue;

package/mcp/dist/data/access.js

@@ -275,7 +275,9 @@ export function removeFinding(phrenPath, project, match) {
         const matched = lines[idx];
         lines.splice(idx, removeCount);
         const normalized = lines.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n";
-        fs.writeFileSync(filePath, normalized);
+        const tmp = filePath + ".tmp." + process.pid;
+        fs.writeFileSync(tmp, normalized);
+        fs.renameSync(tmp, filePath);
         return phrenOk(`Removed from ${project}: ${matched}`);
     });
 }
@@ -323,7 +325,9 @@ export function removeFindings(phrenPath, project, matches) {
         if (removed.length > 0) {
             const filtered = lines.filter((_, i) => !indicesToRemove.has(i));
             const normalized = filtered.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n";
-            fs.writeFileSync(findingsPath, normalized);
+            const tmp = findingsPath + ".tmp." + process.pid;
+            fs.writeFileSync(tmp, normalized);
+            fs.renameSync(tmp, findingsPath);
         }
         return phrenOk({ removed, errors });
     });
@@ -363,7 +367,9 @@ export function editFinding(phrenPath, project, oldText, newText) {
         const metaSuffix = metaMatch ? " " + metaMatch.join(" ") : "";
         lines[idx] = `- ${newTextTrimmed}${metaSuffix}`;
         const normalized = lines.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n";
-        fs.writeFileSync(findingsPath, normalized);
+        const tmp = findingsPath + ".tmp." + process.pid;
+        fs.writeFileSync(tmp, normalized);
+        fs.renameSync(tmp, findingsPath);
         return phrenOk(`Updated finding in ${project}`);
     });
 }
@@ -452,7 +458,10 @@ function withQueueLineOp(phrenPath, project, lineText, op) {
     });
 }
 function writeQueueLines(file, lines) {
-    fs.writeFileSync(file, lines.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n");
+    const content = lines.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n";
+    const tmp = file + ".tmp." + process.pid;
+    fs.writeFileSync(tmp, content);
+    fs.renameSync(tmp, file);
 }
 /** Remove a queue item's line from review.md (finding stays in FINDINGS.md). */
 export function approveQueueItem(phrenPath, project, lineText) {

package/mcp/dist/finding/lifecycle.js

@@ -219,7 +219,9 @@ export function supersedeFinding(phrenPath, project, findingText, supersededBy)
         const today = new Date().toISOString().slice(0, 10);
         lines[matched.data.index] = applyLifecycle(lines[matched.data.index], { status: "superseded", status_updated: today, status_reason: "superseded_by", status_ref: ref }, today, { supersededBy: ref });
         const normalized = lines.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n";
-        fs.writeFileSync(findingsPath, normalized);
+        const tmpPath = findingsPath + ".tmp." + process.pid;
+        fs.writeFileSync(tmpPath, normalized);
+        fs.renameSync(tmpPath, findingsPath);
         return phrenOk({ finding: matched.data.text, superseded_by: ref, status: "superseded" });
     });
 }
@@ -239,7 +241,9 @@ export function retractFinding(phrenPath, project, findingText, reason) {
         const today = new Date().toISOString().slice(0, 10);
         lines[matched.data.index] = applyLifecycle(lines[matched.data.index], { status: "retracted", status_updated: today, status_reason: reasonText }, today);
         const normalized = lines.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n";
-        fs.writeFileSync(findingsPath, normalized);
+        const tmpPath = findingsPath + ".tmp." + process.pid;
+        fs.writeFileSync(tmpPath, normalized);
+        fs.renameSync(tmpPath, findingsPath);
         return phrenOk({ finding: matched.data.text, reason: reasonText, status: "retracted" });
     });
 }
@@ -289,7 +293,9 @@ export function resolveFindingContradiction(phrenPath, project, findingA, findin
             statusB = "retracted";
         }
         const normalized = lines.join("\n").replace(/\n{3,}/g, "\n\n").trimEnd() + "\n";
-        fs.writeFileSync(findingsPath, normalized);
+        const tmpPath = findingsPath + ".tmp." + process.pid;
+        fs.writeFileSync(tmpPath, normalized);
+        fs.renameSync(tmpPath, findingsPath);
         return phrenOk({
             resolution,
             finding_a: { text: matchedA.data.text, status: statusA },

package/mcp/dist/governance/audit.js

@@ -2,18 +2,26 @@ import * as fs from "fs";
 import * as path from "path";
 import { debugLog } from "../shared.js";
 import { errorMessage } from "../utils.js";
+const MAX_LOG_LINES = 1000;
 export function recordRetrieval(phrenPath, file, section) {
     const dir = path.join(phrenPath, ".runtime");
-    fs.mkdirSync(dir, { recursive: true });
-    const logPath = path.join(dir, "retrieval-log.jsonl");
-    const entry = { file, section, retrievedAt: new Date().toISOString() };
-    fs.appendFileSync(logPath, JSON.stringify(entry) + "\n");
+    let logPath;
+    try {
+        fs.mkdirSync(dir, { recursive: true });
+        logPath = path.join(dir, "retrieval-log.jsonl");
+        const entry = { file, section, retrievedAt: new Date().toISOString() };
+        fs.appendFileSync(logPath, JSON.stringify(entry) + "\n");
+    }
+    catch (err) {
+        debugLog(`recordRetrieval write failed: ${errorMessage(err)}`);
+        return;
+    }
     try {
         const stat = fs.statSync(logPath);
         if (stat.size > 500_000) {
             const content = fs.readFileSync(logPath, "utf8");
             const lines = content.split("\n").filter(Boolean);
-            fs.writeFileSync(logPath, lines.slice(-1000).join("\n") + "\n");
+            fs.writeFileSync(logPath, lines.slice(-MAX_LOG_LINES).join("\n") + "\n");
         }
     }
     catch (err) {

package/mcp/dist/governance/policy.js

@@ -8,7 +8,20 @@ import { readProjectConfig } from "../project-config.js";
 import { getActiveProfileDefaults } from "../profile-store.js";
 import { runCustomHooks } from "../hooks.js";
 import { METADATA_REGEX, isCitationLine, isArchiveStart as isArchiveStartMeta, isArchiveEnd as isArchiveEndMeta, stripLifecycleMetadata as stripLifecycleMetadataMeta, } from "../content/metadata.js";
+/** @internal Exported for tests. */
 export const MAX_QUEUE_ENTRY_LENGTH = 500;
+export function buildSyncStatus(opts) {
+    return {
+        ...(opts.pullAt !== undefined ? { lastPullAt: opts.pullAt } : {}),
+        ...(opts.pullStatus !== undefined ? { lastPullStatus: opts.pullStatus } : {}),
+        ...(opts.pullDetail !== undefined ? { lastPullDetail: opts.pullDetail } : {}),
+        ...(opts.successfulPullAt !== undefined ? { lastSuccessfulPullAt: opts.successfulPullAt } : {}),
+        lastPushAt: opts.now,
+        lastPushStatus: opts.pushStatus,
+        ...(opts.pushDetail !== undefined ? { lastPushDetail: opts.pushDetail } : {}),
+        ...(opts.unsyncedCommits !== undefined ? { unsyncedCommits: opts.unsyncedCommits } : {}),
+    };
+}
 export const GOVERNANCE_SCHEMA_VERSION = 1;
 const DEFAULT_POLICY = {
     schemaVersion: GOVERNANCE_SCHEMA_VERSION,

package/mcp/dist/governance/rbac.js

@@ -104,7 +104,7 @@ function rolePermits(role, action) {
  *
  * Returns `{ allowed: true }` when permitted, `{ allowed: false, reason }` when denied.
  */
-export function checkPermission(phrenPath, action, project) {
+function checkPermission(phrenPath, action, project) {
     const actor = (process.env.PHREN_ACTOR ?? "").trim() || null;
     const globalAc = readGlobalAccessControl(phrenPath);
     const projectAccess = project

package/mcp/dist/governance/scores.js

@@ -5,6 +5,7 @@ import { appendAuditLog, debugLog, isRecord, memoryScoresFile, memoryUsageLogFil
 import { withFileLock, isFiniteNumber, hasValidSchemaVersion } from "../shared/governance.js";
 import { errorMessage } from "../utils.js";
 import { logger } from "../logger.js";
+const MAX_LOG_LINES = 1000;
 const GOVERNANCE_SCHEMA_VERSION = 1;
 const DEFAULT_MEMORY_SCORES_FILE = {
     schemaVersion: GOVERNANCE_SCHEMA_VERSION,
@@ -255,7 +256,7 @@ export function recordInjection(phrenPath, key, sessionId) {
         if (stat.size > 1_000_000) {
             const content = fs.readFileSync(logFile, "utf8");
             const lines = content.split("\n");
-            fs.writeFileSync(logFile, lines.slice(-500).join("\n"));
+            fs.writeFileSync(logFile, lines.slice(-MAX_LOG_LINES).join("\n"));
         }
     }
     catch (err) {

package/mcp/dist/hooks.js

@@ -236,7 +236,14 @@ function cachedReadInstallPrefsJson(phrenPath) {
     if (cached && cached.mtimeMs === mtimeMs) {
         return cached.parsed;
     }
-    const parsed = JSON.parse(fs.readFileSync(prefsPath, "utf8"));
+    let parsed;
+    try {
+        parsed = JSON.parse(fs.readFileSync(prefsPath, "utf8"));
+    }
+    catch {
+        _installPrefsJsonCache.delete(prefsPath);
+        return null;
+    }
     _installPrefsJsonCache.set(prefsPath, { mtimeMs, parsed });
     return parsed;
 }
@@ -272,6 +279,7 @@ export const HOOK_EVENT_VALUES = [
     "post-session-end", "post-consolidate",
 ];
 const VALID_HOOK_EVENTS = new Set(HOOK_EVENT_VALUES);
+const MAX_HOOK_COMMAND_LENGTH = 1000;
 /** Return the target (URL or shell command) for display or matching. */
 export function getHookTarget(h) {
     return "webhook" in h ? h.webhook : h.command;
@@ -280,8 +288,8 @@ export function validateCustomHookCommand(command) {
     const trimmed = command.trim();
     if (!trimmed)
         return "Command cannot be empty.";
-    if (trimmed.length > 1000)
-        return "Command too long (max 1000 characters).";
+    if (trimmed.length > MAX_HOOK_COMMAND_LENGTH)
+        return `Command too long (max ${MAX_HOOK_COMMAND_LENGTH} characters).`;
     if (/[`$(){}&|;<>\n\r#]/.test(trimmed)) {
         return "Command contains disallowed shell characters: ` $ ( ) { } & | ; < > # \\n \\r";
     }
@@ -566,7 +574,7 @@ export function configureAllHooks(phrenPath, options = {}) {
             configured.push("Copilot CLI");
         }
         catch (err) {
-            debugLog(`configureAllHooks: copilot failed: ${errorMessage(err)}`);
+            console.warn(`configureAllHooks: copilot hook config failed: ${errorMessage(err)}`);
         }
         if (isToolHookEnabled(phrenPath, "copilot"))
             installSessionWrapper("copilot", phrenPath);
@@ -598,7 +606,7 @@ export function configureAllHooks(phrenPath, options = {}) {
             configured.push("Cursor");
         }
         catch (err) {
-            debugLog(`configureAllHooks: cursor failed: ${errorMessage(err)}`);
+            console.warn(`configureAllHooks: cursor hook config failed: ${errorMessage(err)}`);
         }
         if (isToolHookEnabled(phrenPath, "cursor"))
             installSessionWrapper("cursor", phrenPath);
@@ -629,7 +637,7 @@ export function configureAllHooks(phrenPath, options = {}) {
             configured.push("Codex");
         }
         catch (err) {
-            debugLog(`configureAllHooks: codex failed: ${errorMessage(err)}`);
+            console.warn(`configureAllHooks: codex hook config failed: ${errorMessage(err)}`);
         }
         if (isToolHookEnabled(phrenPath, "codex"))
             installSessionWrapper("codex", phrenPath);

package/mcp/dist/index.js

@@ -72,7 +72,7 @@ async function main() {
     catch (error) {
         const msg = error instanceof Error ? error.message : String(error);
         structuredLog("error", "startup", `Failed to build phren index: ${msg}`);
-        console.error("Failed to build phren index at startup:", error);
+        console.error("Failed to build phren index at startup:", msg);
         process.exit(1);
     }
     let writeQueue = Promise.resolve();

package/mcp/dist/init/init.js

@@ -435,31 +435,26 @@ async function runWalkthrough(phrenPath) {
     log("  Change later: set PHREN_OLLAMA_URL=off to disable");
     let ollamaEnabled = false;
     try {
-        const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("../shared/ollama.js");
-        if (getOllamaUrl()) {
-            const ollamaUp = await checkOllamaAvailable();
-            if (ollamaUp) {
-                const modelReady = await checkModelAvailable();
-                if (modelReady) {
-                    log("  Ollama detected with nomic-embed-text ready.");
-                    ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery?", false);
-                }
-                else {
-                    log("  Ollama detected, but nomic-embed-text is not pulled yet.");
-                    ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery? (will pull nomic-embed-text)", false);
-                    if (ollamaEnabled) {
-                        log("  Run after init: ollama pull nomic-embed-text");
-                    }
-                }
+        const { checkOllamaStatus } = await import("../shared/ollama.js");
+        const status = await checkOllamaStatus();
+        if (status === "ready") {
+            log("  Ollama detected with nomic-embed-text ready.");
+            ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery?", false);
+        }
+        else if (status === "no_model") {
+            log("  Ollama detected, but nomic-embed-text is not pulled yet.");
+            ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery? (will pull nomic-embed-text)", false);
+            if (ollamaEnabled) {
+                log("  Run after init: ollama pull nomic-embed-text");
             }
-            else {
-                log("  Ollama not detected. Install it to enable semantic search:");
-                log("    https://ollama.com  →  then: ollama pull nomic-embed-text");
-                ollamaEnabled = await prompts.confirm("Enable semantic search (Ollama not installed yet)?", false);
-                if (ollamaEnabled) {
-                    log(style.success("  Semantic search enabled — will activate once Ollama is running."));
-                    log("  To disable: set PHREN_OLLAMA_URL=off in your shell profile");
-                }
+        }
+        else if (status === "not_running") {
+            log("  Ollama not detected. Install it to enable semantic search:");
+            log("    https://ollama.com  →  then: ollama pull nomic-embed-text");
+            ollamaEnabled = await prompts.confirm("Enable semantic search (Ollama not installed yet)?", false);
+            if (ollamaEnabled) {
+                log(style.success("  Semantic search enabled — will activate once Ollama is running."));
+                log("  To disable: set PHREN_OLLAMA_URL=off in your shell profile");
             }
         }
     }
@@ -1450,24 +1445,19 @@ export async function runInit(opts = {}) {
     const walkthroughCoveredOllama = Boolean(process.env._PHREN_WALKTHROUGH_OLLAMA_SKIP) || (!hasExistingInstall && !opts.yes);
     if (!walkthroughCoveredOllama) {
         try {
-            const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("../shared/ollama.js");
-            if (getOllamaUrl()) {
-                const ollamaUp = await checkOllamaAvailable();
-                if (ollamaUp) {
-                    const modelReady = await checkModelAvailable();
-                    if (modelReady) {
-                        log("\n  Semantic search: Ollama + nomic-embed-text ready.");
-                    }
-                    else {
-                        log("\n  Semantic search: Ollama running, but nomic-embed-text not pulled.");
-                        log("  Run: ollama pull nomic-embed-text");
-                    }
-                }
-                else {
-                    log("\n  Tip: Install Ollama for semantic search (optional).");
-                    log("  https://ollama.com → then: ollama pull nomic-embed-text");
-                    log("  (Set PHREN_OLLAMA_URL=off to hide this message)");
-                }
+            const { checkOllamaStatus } = await import("../shared/ollama.js");
+            const status = await checkOllamaStatus();
+            if (status === "ready") {
+                log("\n  Semantic search: Ollama + nomic-embed-text ready.");
+            }
+            else if (status === "no_model") {
+                log("\n  Semantic search: Ollama running, but nomic-embed-text not pulled.");
+                log("  Run: ollama pull nomic-embed-text");
+            }
+            else if (status === "not_running") {
+                log("\n  Tip: Install Ollama for semantic search (optional).");
+                log("  https://ollama.com → then: ollama pull nomic-embed-text");
+                log("  (Set PHREN_OLLAMA_URL=off to hide this message)");
             }
         }
         catch (err) {
@@ -2003,6 +1993,28 @@ export async function runUninstall(opts = {}) {
     catch (err) {
         debugLog(`uninstall: cleanup failed for ${contextFile}: ${errorMessage(err)}`);
     }
+    // Remove global CLAUDE.md symlink (created by linkGlobal -> ~/.claude/CLAUDE.md)
+    const globalClaudeLink = homePath(".claude", "CLAUDE.md");
+    try {
+        if (fs.lstatSync(globalClaudeLink).isSymbolicLink()) {
+            fs.unlinkSync(globalClaudeLink);
+            log(`  Removed global CLAUDE.md symlink (${globalClaudeLink})`);
+        }
+    }
+    catch {
+        // Does not exist or not a symlink — nothing to do
+    }
+    // Remove copilot-instructions.md symlink (created by linkGlobal -> ~/.github/copilot-instructions.md)
+    const copilotInstrLink = homePath(".github", "copilot-instructions.md");
+    try {
+        if (fs.lstatSync(copilotInstrLink).isSymbolicLink()) {
+            fs.unlinkSync(copilotInstrLink);
+            log(`  Removed copilot-instructions.md symlink (${copilotInstrLink})`);
+        }
+    }
+    catch {
+        // Does not exist or not a symlink — nothing to do
+    }
     // Sweep agent skill directories for symlinks pointing into the phren store
     if (phrenPath) {
         try {

package/mcp/dist/init/shared.js

@@ -33,7 +33,7 @@ export function commandVersion(cmd, args = ["--version"]) {
         return null;
     }
 }
-export function parseSemverTriple(raw) {
+function parseSemverTriple(raw) {
     const match = raw.match(/(\d+)\.(\d+)\.(\d+)/);
     if (!match)
         return null;

package/mcp/dist/init-bootstrap.js

@@ -1,56 +1,9 @@
 /**
  * Bootstrap-current-project prompting and execution for init.
  */
-import * as path from "path";
 import { debugLog } from "./shared.js";
 import { bootstrapFromExisting, } from "./init/setup.js";
-import { PROJECT_OWNERSHIP_MODES, } from "./project-config.js";
-import { createWalkthroughPrompts, createWalkthroughStyle, } from "./init-walkthrough.js";
-import { getPendingBootstrapTarget } from "./init-detect.js";
 import { log } from "./init/shared.js";
-/**
- * Decide whether to bootstrap the CWD project and with what ownership.
- * May prompt the user interactively.
- */
-export async function resolveBootstrapDecision(phrenPath, opts, ownershipDefault, dryRun) {
-    const pendingBootstrap = getPendingBootstrapTarget(phrenPath, opts);
-    let shouldBootstrap = opts._walkthroughBootstrapCurrentProject === true;
-    let ownership = opts._walkthroughBootstrapOwnership ?? ownershipDefault;
-    if (pendingBootstrap && !dryRun) {
-        const walkthroughAlreadyHandled = opts._walkthroughBootstrapCurrentProject !== undefined;
-        if (walkthroughAlreadyHandled) {
-            shouldBootstrap = opts._walkthroughBootstrapCurrentProject === true;
-            ownership = opts._walkthroughBootstrapOwnership ?? ownershipDefault;
-        }
-        else if (opts.yes || !process.stdin.isTTY || !process.stdout.isTTY) {
-            shouldBootstrap = true;
-            ownership = ownershipDefault;
-        }
-        else {
-            const prompts = await createWalkthroughPrompts();
-            const style = await createWalkthroughStyle();
-            const detectedProjectName = path.basename(pendingBootstrap.path);
-            log("");
-            log(style.header("━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"));
-            log(style.header("Current Project"));
-            log(style.header("━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"));
-            log(`Detected project: ${detectedProjectName}`);
-            shouldBootstrap = await prompts.confirm("Add this project to phren now?", true);
-            if (!shouldBootstrap) {
-                log(style.warning(`  Skipped. Later: cd ${pendingBootstrap.path} && npx phren add`));
-            }
-            else {
-                ownership = await prompts.select("Ownership for detected project", [
-                    { value: ownershipDefault, name: `${ownershipDefault} (default)` },
-                    ...PROJECT_OWNERSHIP_MODES
-                        .filter((mode) => mode !== ownershipDefault)
-                        .map((mode) => ({ value: mode, name: mode })),
-                ], ownershipDefault);
-            }
-        }
-    }
-    return { shouldBootstrap, ownership };
-}
 /**
  * Bootstrap a project from an existing directory into phren.
  */

package/mcp/dist/init-fresh.js

@@ -162,24 +162,19 @@ export async function runFreshInstall(phrenPath, opts, params) {
     const walkthroughCoveredOllama = Boolean(process.env._PHREN_WALKTHROUGH_OLLAMA_SKIP) || !opts.yes;
     if (!walkthroughCoveredOllama) {
         try {
-            const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("./shared/ollama.js");
-            if (getOllamaUrl()) {
-                const ollamaUp = await checkOllamaAvailable();
-                if (ollamaUp) {
-                    const modelReady = await checkModelAvailable();
-                    if (modelReady) {
-                        log("\n  Semantic search: Ollama + nomic-embed-text ready.");
-                    }
-                    else {
-                        log("\n  Semantic search: Ollama running, but nomic-embed-text not pulled.");
-                        log("  Run: ollama pull nomic-embed-text");
-                    }
-                }
-                else {
-                    log("\n  Tip: Install Ollama for semantic search (optional).");
-                    log("  https://ollama.com → then: ollama pull nomic-embed-text");
-                    log("  (Set PHREN_OLLAMA_URL=off to hide this message)");
-                }
+            const { checkOllamaStatus } = await import("./shared/ollama.js");
+            const status = await checkOllamaStatus();
+            if (status === "ready") {
+                log("\n  Semantic search: Ollama + nomic-embed-text ready.");
+            }
+            else if (status === "no_model") {
+                log("\n  Semantic search: Ollama running, but nomic-embed-text not pulled.");
+                log("  Run: ollama pull nomic-embed-text");
+            }
+            else if (status === "not_running") {
+                log("\n  Tip: Install Ollama for semantic search (optional).");
+                log("  https://ollama.com → then: ollama pull nomic-embed-text");
+                log("  (Set PHREN_OLLAMA_URL=off to hide this message)");
             }
         }
         catch (err) {

package/mcp/dist/init-uninstall.js

@@ -428,6 +428,28 @@ export async function runUninstall(opts = {}) {
     catch (err) {
         debugLog(`uninstall: cleanup failed for ${contextFile}: ${errorMessage(err)}`);
     }
+    // Remove global CLAUDE.md symlink (created by linkGlobal -> ~/.claude/CLAUDE.md)
+    const globalClaudeLink = homePath(".claude", "CLAUDE.md");
+    try {
+        if (fs.lstatSync(globalClaudeLink).isSymbolicLink()) {
+            fs.unlinkSync(globalClaudeLink);
+            log(`  Removed global CLAUDE.md symlink (${globalClaudeLink})`);
+        }
+    }
+    catch {
+        // Does not exist or not a symlink — nothing to do
+    }
+    // Remove copilot-instructions.md symlink (created by linkGlobal -> ~/.github/copilot-instructions.md)
+    const copilotInstrLink = homePath(".github", "copilot-instructions.md");
+    try {
+        if (fs.lstatSync(copilotInstrLink).isSymbolicLink()) {
+            fs.unlinkSync(copilotInstrLink);
+            log(`  Removed copilot-instructions.md symlink (${copilotInstrLink})`);
+        }
+    }
+    catch {
+        // Does not exist or not a symlink — nothing to do
+    }
     // Sweep agent skill directories for symlinks pointing into the phren store
     if (phrenPath) {
         try {

package/mcp/dist/init-walkthrough.js

@@ -300,31 +300,26 @@ export async function runWalkthrough(phrenPath) {
     log("  Change later: set PHREN_OLLAMA_URL=off to disable");
     let ollamaEnabled = false;
     try {
-        const { checkOllamaAvailable, checkModelAvailable, getOllamaUrl } = await import("./shared/ollama.js");
-        if (getOllamaUrl()) {
-            const ollamaUp = await checkOllamaAvailable();
-            if (ollamaUp) {
-                const modelReady = await checkModelAvailable();
-                if (modelReady) {
-                    log("  Ollama detected with nomic-embed-text ready.");
-                    ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery?", false);
-                }
-                else {
-                    log("  Ollama detected, but nomic-embed-text is not pulled yet.");
-                    ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery? (will pull nomic-embed-text)", false);
-                    if (ollamaEnabled) {
-                        log("  Run after init: ollama pull nomic-embed-text");
-                    }
-                }
+        const { checkOllamaStatus } = await import("./shared/ollama.js");
+        const status = await checkOllamaStatus();
+        if (status === "ready") {
+            log("  Ollama detected with nomic-embed-text ready.");
+            ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery?", false);
+        }
+        else if (status === "no_model") {
+            log("  Ollama detected, but nomic-embed-text is not pulled yet.");
+            ollamaEnabled = await prompts.confirm("Enable semantic search for fuzzy/paraphrase recovery? (will pull nomic-embed-text)", false);
+            if (ollamaEnabled) {
+                log("  Run after init: ollama pull nomic-embed-text");
             }
-            else {
-                log("  Ollama not detected. Install it to enable semantic search:");
-                log("    https://ollama.com  →  then: ollama pull nomic-embed-text");
-                ollamaEnabled = await prompts.confirm("Enable semantic search (Ollama not installed yet)?", false);
-                if (ollamaEnabled) {
-                    log(style.success("  Semantic search enabled — will activate once Ollama is running."));
-                    log("  To disable: set PHREN_OLLAMA_URL=off in your shell profile");
-                }
+        }
+        else if (status === "not_running") {
+            log("  Ollama not detected. Install it to enable semantic search:");
+            log("    https://ollama.com  →  then: ollama pull nomic-embed-text");
+            ollamaEnabled = await prompts.confirm("Enable semantic search (Ollama not installed yet)?", false);
+            if (ollamaEnabled) {
+                log(style.success("  Semantic search enabled — will activate once Ollama is running."));
+                log("  To disable: set PHREN_OLLAMA_URL=off in your shell profile");
             }
         }
     }