@phren/cli 0.0.28 → 0.0.33

package/mcp/dist/cli-hooks-stop.js

@@ -0,0 +1,519 @@
+/**
+ * Stop hook handler: git commit/push, background sync, auto-capture, governance.
+ * Extracted from cli-hooks-session.ts for modularity.
+ */
+import { buildHookContext, handleGuardSkip, debugLog, runtimeFile, sessionMarker, getPhrenPath, updateRuntimeHealth, buildSyncStatus, appendAuditLog, withFileLock, getWorkflowPolicy, isProjectHookEnabled, ensureLocalGitRepo, getProactivityLevelForTask, getProactivityLevelForFindings, hasExplicitFindingSignal, shouldAutoCaptureFindingsForLevel, FINDING_SENSITIVITY_CONFIG, isFeatureEnabled, errorMessage, bootstrapPhrenDotEnv, finalizeTaskSession, appendFindingJournal, homePath, } from "./cli/hooks-context.js";
+import * as fs from "fs";
+import * as path from "path";
+import * as os from "os";
+import { spawnDetachedChild } from "./shared/process.js";
+import { resolveSubprocessArgs as _resolveSubprocessArgs, runBestEffortGit, countUnsyncedCommits, recoverPushConflict, } from "./cli-hooks-git.js";
+import { logger } from "./logger.js";
+const SYNC_LOCK_STALE_MS = 10 * 60 * 1000; // 10 minutes
+/** Read JSON from stdin if it's not a TTY. Returns null if stdin is a TTY or parsing fails. */
+export function readStdinJson() {
+    if (process.stdin.isTTY)
+        return null;
+    try {
+        return JSON.parse(fs.readFileSync(0, "utf-8"));
+    }
+    catch (err) {
+        logger.debug("readStdinJson", errorMessage(err));
+        return null;
+    }
+}
+/** Validate that a transcript path points to a safe, expected location.
+ * Uses realpathSync to dereference symlinks, preventing traversal attacks
+ * where a symlink inside a safe dir points outside it.
+ */
+function isSafeTranscriptPath(p) {
+    // Resolve symlinks so a link like ~/.claude/evil -> /etc/passwd is caught
+    let normalized;
+    try {
+        normalized = fs.realpathSync.native(p);
+    }
+    catch {
+        // If the file doesn't exist yet, fall back to lexical resolution
+        try {
+            normalized = fs.realpathSync.native(path.dirname(p));
+            normalized = path.join(normalized, path.basename(p));
+        }
+        catch {
+            normalized = path.resolve(p);
+        }
+    }
+    const safePrefixes = [
+        path.resolve(os.tmpdir()),
+        path.resolve(homePath(".claude")),
+        path.resolve(homePath(".config", "claude")),
+    ];
+    return safePrefixes.some(prefix => normalized.startsWith(prefix + path.sep) || normalized === prefix);
+}
+// ── Q21: Conversation memory capture ─────────────────────────────────────────
+const INSIGHT_KEYWORDS = [
+    "always", "never", "important", "pitfall", "gotcha", "trick", "workaround",
+    "careful", "caveat", "beware", "note that", "make sure",
+    "don't forget", "remember to", "must", "avoid", "prefer",
+];
+const INSIGHT_KEYWORD_RE = new RegExp(`\\b(${INSIGHT_KEYWORDS.join("|")})\\b`, "i");
+/**
+ * Extract potential insights from conversation text using keyword heuristics.
+ * Returns lines that contain insight-signal words and look like actionable knowledge.
+ */
+export function extractConversationInsights(text) {
+    const lines = text.split("\n").filter(l => l.trim().length > 20 && l.trim().length < 300);
+    const insights = [];
+    const seen = new Set();
+    for (const line of lines) {
+        const trimmed = line.trim();
+        // Skip code-only lines, headers, etc.
+        if (trimmed.startsWith("```") || trimmed.startsWith("#") || trimmed.startsWith("//"))
+            continue;
+        if (trimmed.startsWith("$") || trimmed.startsWith(">"))
+            continue;
+        if (INSIGHT_KEYWORD_RE.test(trimmed) || hasExplicitFindingSignal(trimmed)) {
+            // Normalize for dedup
+            const normalized = trimmed.toLowerCase().replace(/\s+/g, " ");
+            if (!seen.has(normalized)) {
+                seen.add(normalized);
+                insights.push(trimmed);
+            }
+        }
+    }
+    // Cap to prevent flooding
+    return insights.slice(0, 5);
+}
+export function filterConversationInsightsForProactivity(insights, level = getProactivityLevelForFindings(getPhrenPath())) {
+    if (level === "high")
+        return insights;
+    return insights.filter((insight) => shouldAutoCaptureFindingsForLevel(level, insight));
+}
+export function getSessionCap() {
+    if (process.env.PHREN_AUTOCAPTURE_SESSION_CAP) {
+        return parseInt(process.env.PHREN_AUTOCAPTURE_SESSION_CAP, 10);
+    }
+    try {
+        const policy = getWorkflowPolicy(getPhrenPath());
+        const sensitivity = policy.findingSensitivity ?? "balanced";
+        return FINDING_SENSITIVITY_CONFIG[sensitivity]?.sessionCap ?? 10;
+    }
+    catch {
+        return 10;
+    }
+}
+function scheduleBackgroundSync(phrenPathLocal) {
+    const lockPath = runtimeFile(phrenPathLocal, "background-sync.lock");
+    const logPath = runtimeFile(phrenPathLocal, "background-sync.log");
+    const spawnArgs = _resolveSubprocessArgs("background-sync");
+    if (!spawnArgs)
+        return false;
+    try {
+        if (fs.existsSync(lockPath)) {
+            const ageMs = Date.now() - fs.statSync(lockPath).mtimeMs;
+            if (ageMs <= SYNC_LOCK_STALE_MS)
+                return false;
+            fs.unlinkSync(lockPath);
+        }
+    }
+    catch (err) {
+        debugLog(`scheduleBackgroundSync: lock check failed: ${errorMessage(err)}`);
+        return false;
+    }
+    try {
+        fs.writeFileSync(lockPath, JSON.stringify({ startedAt: new Date().toISOString(), pid: process.pid }) + "\n", { flag: "wx" });
+        const logFd = fs.openSync(logPath, "a");
+        fs.writeSync(logFd, `[${new Date().toISOString()}] spawn ${process.execPath} ${spawnArgs.join(" ")}\n`);
+        const child = spawnDetachedChild(spawnArgs, { phrenPath: phrenPathLocal, logFd });
+        child.unref();
+        fs.closeSync(logFd);
+        return true;
+    }
+    catch (err) {
+        try {
+            fs.unlinkSync(lockPath);
+        }
+        catch { }
+        debugLog(`scheduleBackgroundSync: spawn failed: ${errorMessage(err)}`);
+        return false;
+    }
+}
+function scheduleWeeklyGovernance() {
+    try {
+        const lastGovPath = runtimeFile(getPhrenPath(), "last-governance.txt");
+        const lastRun = fs.existsSync(lastGovPath) ? parseInt(fs.readFileSync(lastGovPath, "utf8"), 10) : 0;
+        const daysSince = (Date.now() - lastRun) / 86_400_000;
+        if (daysSince >= 7) {
+            const spawnArgs = _resolveSubprocessArgs("background-maintenance");
+            if (spawnArgs) {
+                const child = spawnDetachedChild(spawnArgs, { phrenPath: getPhrenPath() });
+                child.unref();
+                fs.writeFileSync(lastGovPath, Date.now().toString());
+                debugLog("hook_stop: scheduled weekly governance run");
+            }
+        }
+    }
+    catch (err) {
+        debugLog(`hook_stop: governance scheduling failed: ${errorMessage(err)}`);
+    }
+}
+export async function handleHookStop() {
+    const ctx = buildHookContext();
+    const { phrenPath, activeProject, manifest } = ctx;
+    const now = new Date().toISOString();
+    bootstrapPhrenDotEnv(phrenPath);
+    if (!ctx.hooksEnabled) {
+        handleGuardSkip(ctx, "hook_stop", "disabled", {
+            lastStopAt: now,
+            lastAutoSave: { at: now, status: "clean", detail: "hooks disabled by preference" },
+        });
+        return;
+    }
+    if (!ctx.toolHookEnabled) {
+        handleGuardSkip(ctx, "hook_stop", `tool_disabled tool=${ctx.hookTool}`);
+        return;
+    }
+    if (!isProjectHookEnabled(phrenPath, activeProject, "Stop")) {
+        handleGuardSkip(ctx, "hook_stop", `project_disabled project=${activeProject}`, {
+            lastStopAt: now,
+            lastAutoSave: { at: now, status: "clean", detail: `hooks disabled for project ${activeProject}` },
+        });
+        return;
+    }
+    // Read stdin early — it's a stream and can only be consumed once.
+    // Needed for auto-capture transcript_path parsing.
+    const stdinPayload = readStdinJson();
+    const taskSessionId = typeof stdinPayload?.session_id === "string" ? stdinPayload.session_id : undefined;
+    const taskLevel = getProactivityLevelForTask(phrenPath);
+    if (taskSessionId && taskLevel !== "high") {
+        debugLog(`hook-stop task proactivity=${taskLevel}`);
+    }
+    // Auto-capture BEFORE git operations so captured insights get committed and pushed.
+    // Gated behind PHREN_FEATURE_AUTO_CAPTURE=1.
+    const findingsLevel = getProactivityLevelForFindings(phrenPath);
+    if (isFeatureEnabled("PHREN_FEATURE_AUTO_CAPTURE", false) && findingsLevel !== "low") {
+        try {
+            let captureInput = process.env.PHREN_CONVERSATION_CONTEXT || "";
+            if (!captureInput && stdinPayload?.transcript_path) {
+                const transcriptPath = stdinPayload.transcript_path;
+                if (!isSafeTranscriptPath(transcriptPath)) {
+                    debugLog(`auto-capture: skipping unsafe transcript_path: ${transcriptPath}`);
+                }
+                else if (fs.existsSync(transcriptPath)) {
+                    // Cap at last 500 lines (~50 KB) to bound memory usage for long sessions
+                    const raw = fs.readFileSync(transcriptPath, "utf-8");
+                    const allLines = raw.split("\n").filter(Boolean);
+                    const lines = allLines.length > 500 ? allLines.slice(-500) : allLines;
+                    const assistantTexts = [];
+                    for (const line of lines) {
+                        try {
+                            const msg = JSON.parse(line);
+                            if (msg.role !== "assistant")
+                                continue;
+                            if (typeof msg.content === "string")
+                                assistantTexts.push(msg.content);
+                            else if (Array.isArray(msg.content)) {
+                                for (const block of msg.content) {
+                                    if (block.type === "text" && block.text)
+                                        assistantTexts.push(block.text);
+                                }
+                            }
+                        }
+                        catch (err) {
+                            logger.debug("hookStop transcriptParse", errorMessage(err));
+                        }
+                    }
+                    captureInput = assistantTexts.join("\n");
+                }
+            }
+            if (captureInput) {
+                if (activeProject) {
+                    // Check session cap before extracting — same guard as PostToolUse hook
+                    let capReached = false;
+                    if (taskSessionId) {
+                        try {
+                            const capFile = sessionMarker(phrenPath, `tool-findings-${taskSessionId}`);
+                            let count = 0;
+                            if (fs.existsSync(capFile)) {
+                                count = Number.parseInt(fs.readFileSync(capFile, "utf8").trim(), 10) || 0;
+                            }
+                            const cap = getSessionCap();
+                            if (count >= cap) {
+                                debugLog(`hook-stop: session cap reached (${count}/${cap}), skipping extraction`);
+                                capReached = true;
+                            }
+                        }
+                        catch (err) {
+                            logger.debug("hookStop sessionCapCheck", errorMessage(err));
+                        }
+                    }
+                    if (!capReached) {
+                        const insights = filterConversationInsightsForProactivity(extractConversationInsights(captureInput), findingsLevel);
+                        for (const insight of insights) {
+                            appendFindingJournal(phrenPath, activeProject, `[pattern] ${insight}`, {
+                                source: "hook",
+                                sessionId: `hook-stop-${Date.now()}`,
+                            });
+                            debugLog(`auto-capture: saved insight for ${activeProject}: ${insight.slice(0, 60)}`);
+                        }
+                    }
+                }
+            }
+        }
+        catch (err) {
+            debugLog(`auto-capture failed: ${errorMessage(err)}`);
+        }
+    }
+    else if (isFeatureEnabled("PHREN_FEATURE_AUTO_CAPTURE", false)) {
+        debugLog("auto-capture: skipped because findings proactivity is low");
+    }
+    // Wrap git operations in a file lock to prevent concurrent agents from fighting
+    const gitOpLockPath = path.join(phrenPath, ".runtime", "git-op");
+    await withFileLock(gitOpLockPath, async () => {
+        if (manifest?.installMode === "project-local") {
+            updateRuntimeHealth(phrenPath, {
+                lastStopAt: now,
+                lastAutoSave: { at: now, status: "saved-local", detail: "project-local mode writes files only" },
+                lastSync: {
+                    lastPushAt: now,
+                    lastPushStatus: "saved-local",
+                    lastPushDetail: "project-local mode does not manage git sync",
+                },
+            });
+            appendAuditLog(phrenPath, "hook_stop", "status=skipped-local");
+            return;
+        }
+        const gitRepo = ensureLocalGitRepo(phrenPath);
+        if (!gitRepo.ok) {
+            finalizeTaskSession({
+                phrenPath,
+                sessionId: taskSessionId,
+                status: "error",
+                detail: gitRepo.detail,
+            });
+            updateRuntimeHealth(phrenPath, {
+                lastStopAt: now,
+                lastAutoSave: { at: now, status: "error", detail: gitRepo.detail },
+                lastSync: {
+                    lastPushAt: now,
+                    lastPushStatus: "error",
+                    lastPushDetail: gitRepo.detail,
+                },
+            });
+            appendAuditLog(phrenPath, "hook_stop", `status=error detail=${JSON.stringify(gitRepo.detail)}`);
+            process.stderr.write(`phren: git repo error — ${gitRepo.detail}. Run 'phren doctor --fix' for details.\n`);
+            return;
+        }
+        const status = await runBestEffortGit(["status", "--porcelain"], phrenPath);
+        if (!status.ok) {
+            finalizeTaskSession({
+                phrenPath,
+                sessionId: taskSessionId,
+                status: "error",
+                detail: status.error || "git status failed",
+            });
+            updateRuntimeHealth(phrenPath, {
+                lastStopAt: now,
+                lastAutoSave: { at: now, status: "error", detail: status.error || "git status failed" },
+                lastSync: {
+                    lastPushAt: now,
+                    lastPushStatus: "error",
+                    lastPushDetail: status.error || "git status failed",
+                },
+            });
+            appendAuditLog(phrenPath, "hook_stop", `status=error detail=${JSON.stringify(status.error || "git status failed")}`);
+            process.stderr.write(`phren: git status failed — your changes may not be saved. Run 'phren doctor --fix'.\n`);
+            return;
+        }
+        if (!status.output) {
+            updateRuntimeHealth(phrenPath, {
+                lastStopAt: now,
+                lastAutoSave: { at: now, status: "clean", detail: "no changes" },
+                lastSync: {
+                    lastPushAt: now,
+                    lastPushStatus: "saved-pushed",
+                    lastPushDetail: "no changes",
+                    unsyncedCommits: 0,
+                },
+            });
+            appendAuditLog(phrenPath, "hook_stop", "status=clean");
+            return;
+        }
+        // Stage all changes first, then unstage any sensitive files that slipped
+        // through. Using pathspec exclusions with `git add -A` can fail when
+        // excluded paths are also gitignored (git treats the pathspec as an error).
+        let add = await runBestEffortGit(["add", "-A"], phrenPath);
+        if (add.ok) {
+            // Belt-and-suspenders: unstage sensitive files that .gitignore should
+            // already block. Failures here are non-fatal (files may not exist).
+            await runBestEffortGit(["reset", "HEAD", "--", ".env", "**/.env", "*.pem", "*.key"], phrenPath);
+        }
+        let commitMsg = "auto-save phren";
+        if (add.ok) {
+            const diff = await runBestEffortGit(["diff", "--cached", "--stat", "--no-color"], phrenPath);
+            if (diff.ok && diff.output) {
+                // Parse "project/file.md | 3 +++" lines into project names and file types
+                const changes = new Map();
+                for (const line of diff.output.split("\n")) {
+                    const m = line.match(/^\s*([^/]+)\/([^|]+)\s*\|/);
+                    if (!m)
+                        continue;
+                    const proj = m[1].trim();
+                    if (proj.startsWith("."))
+                        continue; // skip .config, .runtime, etc.
+                    const file = m[2].trim();
+                    if (!changes.has(proj))
+                        changes.set(proj, new Set());
+                    if (/findings/i.test(file))
+                        changes.get(proj).add("findings");
+                    else if (/tasks/i.test(file))
+                        changes.get(proj).add("task");
+                    else if (/CLAUDE/i.test(file))
+                        changes.get(proj).add("config");
+                    else if (/summary/i.test(file))
+                        changes.get(proj).add("summary");
+                    else if (/skill/i.test(file))
+                        changes.get(proj).add("skills");
+                    else if (/reference/i.test(file))
+                        changes.get(proj).add("reference");
+                    else
+                        changes.get(proj).add("update");
+                }
+                if (changes.size > 0) {
+                    const parts = [...changes.entries()].map(([proj, types]) => `${proj}(${[...types].join(",")})`);
+                    commitMsg = `phren: ${parts.join(" ")}`;
+                }
+            }
+        }
+        const commit = add.ok ? await runBestEffortGit(["commit", "-m", commitMsg], phrenPath) : { ok: false, error: add.error };
+        if (!add.ok || !commit.ok) {
+            finalizeTaskSession({
+                phrenPath,
+                sessionId: taskSessionId,
+                status: "error",
+                detail: add.error || commit.error || "git add/commit failed",
+            });
+            updateRuntimeHealth(phrenPath, {
+                lastStopAt: now,
+                lastAutoSave: {
+                    at: now,
+                    status: "error",
+                    detail: add.error || commit.error || "git add/commit failed",
+                },
+                lastSync: {
+                    lastPushAt: now,
+                    lastPushStatus: "error",
+                    lastPushDetail: add.error || commit.error || "git add/commit failed",
+                },
+            });
+            appendAuditLog(phrenPath, "hook_stop", `status=error detail=${JSON.stringify(add.error || commit.error || "git add/commit failed")}`);
+            process.stderr.write(`phren: git commit failed — ${add.error || commit.error || "unknown error"}. Changes not saved.\n`);
+            return;
+        }
+        const remotes = await runBestEffortGit(["remote"], phrenPath);
+        if (!remotes.ok || !remotes.output) {
+            finalizeTaskSession({
+                phrenPath,
+                sessionId: taskSessionId,
+                status: "saved-local",
+                detail: "commit created; no remote configured",
+            });
+            const unsyncedCommits = await countUnsyncedCommits(phrenPath);
+            updateRuntimeHealth(phrenPath, {
+                lastStopAt: now,
+                lastAutoSave: { at: now, status: "saved-local", detail: "commit created; no remote configured" },
+                lastSync: {
+                    lastPushAt: now,
+                    lastPushStatus: "saved-local",
+                    lastPushDetail: "commit created; no remote configured",
+                    unsyncedCommits,
+                },
+            });
+            appendAuditLog(phrenPath, "hook_stop", "status=saved-local");
+            if (unsyncedCommits > 3) {
+                process.stderr.write(`phren: ${unsyncedCommits} unsynced commits — no git remote configured.\n`);
+            }
+            return;
+        }
+        const unsyncedCommits = await countUnsyncedCommits(phrenPath);
+        const scheduled = scheduleBackgroundSync(phrenPath);
+        const syncDetail = scheduled
+            ? "commit saved; background sync scheduled"
+            : "commit saved; background sync already running";
+        finalizeTaskSession({
+            phrenPath,
+            sessionId: taskSessionId,
+            status: "saved-local",
+            detail: syncDetail,
+        });
+        updateRuntimeHealth(phrenPath, {
+            lastStopAt: now,
+            lastAutoSave: { at: now, status: "saved-local", detail: syncDetail },
+            lastSync: {
+                lastPushAt: now,
+                lastPushStatus: "saved-local",
+                lastPushDetail: syncDetail,
+                unsyncedCommits,
+            },
+        });
+        appendAuditLog(phrenPath, "hook_stop", `status=saved-local detail=${JSON.stringify(syncDetail)}`);
+    }); // end withFileLock(gitOpLockPath)
+    // Auto governance scheduling (non-blocking)
+    scheduleWeeklyGovernance();
+}
+export async function handleBackgroundSync() {
+    const phrenPathLocal = getPhrenPath();
+    const now = new Date().toISOString();
+    const lockPath = runtimeFile(phrenPathLocal, "background-sync.lock");
+    try {
+        const remotes = await runBestEffortGit(["remote"], phrenPathLocal);
+        if (!remotes.ok || !remotes.output) {
+            const unsyncedCommits = await countUnsyncedCommits(phrenPathLocal);
+            updateRuntimeHealth(phrenPathLocal, {
+                lastAutoSave: { at: now, status: "saved-local", detail: "background sync skipped; no remote configured" },
+                lastSync: buildSyncStatus({ now, pushStatus: "saved-local", pushDetail: "background sync skipped; no remote configured", unsyncedCommits }),
+            });
+            appendAuditLog(phrenPathLocal, "background_sync", "status=saved-local detail=no_remote");
+            return;
+        }
+        const push = await runBestEffortGit(["push"], phrenPathLocal);
+        if (push.ok) {
+            updateRuntimeHealth(phrenPathLocal, {
+                lastAutoSave: { at: now, status: "saved-pushed", detail: "commit pushed by background sync" },
+                lastSync: buildSyncStatus({ now, pushStatus: "saved-pushed", pushDetail: "commit pushed by background sync", unsyncedCommits: 0 }),
+            });
+            appendAuditLog(phrenPathLocal, "background_sync", "status=saved-pushed");
+            return;
+        }
+        const recovered = await recoverPushConflict(phrenPathLocal);
+        if (recovered.ok) {
+            updateRuntimeHealth(phrenPathLocal, {
+                lastAutoSave: { at: now, status: "saved-pushed", detail: recovered.detail },
+                lastSync: buildSyncStatus({ now, pushStatus: "saved-pushed", pushDetail: recovered.detail, pullAt: now, pullStatus: recovered.pullStatus, pullDetail: recovered.pullDetail, successfulPullAt: now, unsyncedCommits: 0 }),
+            });
+            appendAuditLog(phrenPathLocal, "background_sync", `status=saved-pushed detail=${JSON.stringify(recovered.detail)}`);
+            return;
+        }
+        const unsyncedCommits = await countUnsyncedCommits(phrenPathLocal);
+        const failDetail = recovered.detail || push.error || "background sync push failed";
+        updateRuntimeHealth(phrenPathLocal, {
+            lastAutoSave: { at: now, status: "saved-local", detail: failDetail },
+            lastSync: buildSyncStatus({ now, pushStatus: "saved-local", pushDetail: failDetail, pullAt: now, pullStatus: recovered.pullStatus, pullDetail: recovered.pullDetail, unsyncedCommits }),
+        });
+        appendAuditLog(phrenPathLocal, "background_sync", `status=saved-local detail=${JSON.stringify(failDetail)}`);
+        // Append to sync-warnings.jsonl so health_check and session_start can surface recent failures
+        try {
+            const warningsPath = runtimeFile(phrenPathLocal, "sync-warnings.jsonl");
+            const entry = JSON.stringify({ at: now, error: failDetail, unsyncedCommits }) + "\n";
+            fs.appendFileSync(warningsPath, entry);
+        }
+        catch (err) {
+            debugLog(`background-sync: failed to write sync warning: ${errorMessage(err)}`);
+        }
+    }
+    finally {
+        try {
+            fs.unlinkSync(lockPath);
+        }
+        catch { }
+    }
+}

package/mcp/dist/{content-archive.js → content/archive.js}

@@ -1,11 +1,13 @@
 import * as fs from "fs";
 import * as path from "path";
 import * as crypto from "crypto";
-import { debugLog, runtimeFile, phrenOk, phrenErr, PhrenError, appendAuditLog, tryUnlink } from "./shared.js";
-import { isValidProjectName, safeProjectPath, errorMessage } from "./utils.js";
-import { withFileLock } from "./shared-governance.js";
-import { appendArchivedEntriesToTopicDoc, classifyTopicForText, readProjectTopics, topicReferencePath } from "./project-topics.js";
-import { isCitationLine, isArchiveStart, isArchiveEnd, stripComments } from "./content-metadata.js";
+import { debugLog, runtimeFile, phrenOk, phrenErr, PhrenError, appendAuditLog, tryUnlink } from "../shared.js";
+import { isValidProjectName, safeProjectPath, errorMessage } from "../utils.js";
+import { withFileLock } from "../shared/governance.js";
+import { walkDirectory } from "../shared/data-utils.js";
+import { appendArchivedEntriesToTopicDoc, classifyTopicForText, readProjectTopics, topicReferencePath } from "../project-topics.js";
+import { isCitationLine, isArchiveStart, isArchiveEnd, stripComments } from "./metadata.js";
+import { logger } from "../logger.js";
 /**
  * Count active (non-archived) finding entries in FINDINGS.md content.
  * Entries inside archive blocks are considered archived.
@@ -80,34 +82,20 @@ function parseActiveEntries(content) {
 /** Build a Set of normalized bullet strings from all .md files in referenceDir. */
 function buildArchivedBulletSet(referenceDir) {
     const bulletSet = new Set();
-    if (!fs.existsSync(referenceDir))
-        return bulletSet;
     try {
-        const stack = [referenceDir];
-        while (stack.length > 0) {
-            const current = stack.pop();
-            for (const entry of fs.readdirSync(current, { withFileTypes: true })) {
-                const fullPath = path.join(current, entry.name);
-                if (entry.isDirectory()) {
-                    stack.push(fullPath);
+        for (const filePath of walkDirectory(referenceDir)) {
+            const content = fs.readFileSync(filePath, "utf8");
+            for (const line of content.split("\n")) {
+                if (!line.startsWith("- "))
                     continue;
-                }
-                if (!entry.isFile() || !entry.name.endsWith(".md"))
-                    continue;
-                const content = fs.readFileSync(fullPath, "utf8");
-                for (const line of content.split("\n")) {
-                    if (!line.startsWith("- "))
-                        continue;
-                    const normalizedLine = stripComments(line).replace(/^-\s+/, "").trim().toLowerCase();
-                    if (normalizedLine)
-                        bulletSet.add(normalizedLine);
-                }
+                const normalizedLine = stripComments(line).replace(/^-\s+/, "").trim().toLowerCase();
+                if (normalizedLine)
+                    bulletSet.add(normalizedLine);
             }
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] buildArchivedBulletSet: ${errorMessage(err)}\n`);
+        logger.debug("archive", `buildArchivedBulletSet: ${errorMessage(err)}`);
     }
     return bulletSet;
 }
@@ -280,8 +268,7 @@ export function autoArchiveToReference(phrenPath, project, keepCount) {
             fs.unlinkSync(lockFile);
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG))
-                process.stderr.write(`[phren] autoArchiveToReference unlockFile: ${errorMessage(err)}\n`);
+            logger.debug("archive", `autoArchiveToReference unlockFile: ${errorMessage(err)}`);
         }
     }
 }

package/mcp/dist/{content-citation.js → content/citation.js}

@@ -1,10 +1,10 @@
 import * as fs from "fs";
 import * as path from "path";
-import { debugLog, EXEC_TIMEOUT_MS, EXEC_TIMEOUT_QUICK_MS } from "./shared.js";
-import { errorMessage, runGitOrThrow } from "./utils.js";
-import { findingIdFromLine } from "./finding-impact.js";
-import { METADATA_REGEX, isArchiveStart, isArchiveEnd } from "./content-metadata.js";
-import { FINDING_TYPE_DECAY, extractFindingType } from "./finding-lifecycle.js";
+import { debugLog, EXEC_TIMEOUT_MS, EXEC_TIMEOUT_QUICK_MS } from "../shared.js";
+import { errorMessage, runGitOrThrow } from "../utils.js";
+import { findingIdFromLine } from "../finding/impact.js";
+import { METADATA_REGEX, isArchiveStart, isArchiveEnd } from "./metadata.js";
+import { FINDING_TYPE_DECAY, extractFindingType } from "../finding/lifecycle.js";
 export const FINDING_PROVENANCE_SOURCES = [
     "human",
     "agent",

package/mcp/dist/{content-dedup.js → content/dedup.js}

@@ -1,10 +1,11 @@
 import * as fs from "fs";
 import * as path from "path";
 import * as crypto from "crypto";
-import { debugLog, runtimeFile, KNOWN_OBSERVATION_TAGS } from "./shared.js";
-import { isFeatureEnabled, safeProjectPath, errorMessage } from "./utils.js";
-import { UNIVERSAL_TECH_TERMS_RE, EXTRA_ENTITY_PATTERNS } from "./phren-core.js";
-import { isInactiveFindingLine } from "./finding-lifecycle.js";
+import { debugLog, runtimeFile, KNOWN_OBSERVATION_TAGS } from "../shared.js";
+import { isFeatureEnabled, safeProjectPath, errorMessage } from "../utils.js";
+import { UNIVERSAL_TECH_TERMS_RE, EXTRA_ENTITY_PATTERNS } from "../phren-core.js";
+import { isInactiveFindingLine } from "../finding/lifecycle.js";
+import { logger } from "../logger.js";
 // ── LLM provider abstraction ────────────────────────────────────────────────
 const MAX_CACHE_ENTRIES = 500;
 function loadCache(cachePath) {
@@ -50,8 +51,7 @@ async function withCache(cachePath, key, ttlMs, compute) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] withCache load (${path.basename(cachePath)}): ${errorMessage(err)}\n`);
+        logger.debug("dedup", `withCache load (${path.basename(cachePath)}): ${errorMessage(err)}`);
     }
     const result = await compute();
     // Persist result
@@ -61,8 +61,7 @@ async function withCache(cachePath, key, ttlMs, compute) {
         persistCache(cachePath, cache);
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] withCache persist (${path.basename(cachePath)}): ${errorMessage(err)}\n`);
+        logger.debug("dedup", `withCache persist (${path.basename(cachePath)}): ${errorMessage(err)}`);
     }
     return result;
 }
@@ -562,8 +561,7 @@ export async function checkSemanticConflicts(phrenPath, project, newFinding, sig
                 return { name: e.name, mtime: fs.statSync(fp).mtimeMs, fp };
             }
             catch (err) {
-                if ((process.env.PHREN_DEBUG))
-                    process.stderr.write(`[phren] crossProjectScan stat: ${errorMessage(err)}\n`);
+                logger.debug("dedup", `crossProjectScan stat: ${errorMessage(err)}`);
                 return null;
             }
         })
@@ -577,8 +575,7 @@ export async function checkSemanticConflicts(phrenPath, project, newFinding, sig
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG))
-            process.stderr.write(`[phren] crossProjectScan: ${errorMessage(err)}\n`);
+        logger.debug("dedup", `crossProjectScan: ${errorMessage(err)}`);
     }
     const annotations = [];
     const deadline = Date.now() + CONFLICT_CHECK_TOTAL_TIMEOUT_MS;