@phren/cli 0.0.9 → 0.0.10

package/mcp/dist/cli-govern.js

@@ -227,6 +227,167 @@ export async function handleConsolidateMemories(args = []) {
         return;
     console.log(`Updated backups (${backups.length}): ${backups.join(", ")}`);
 }
+export async function handleGcMaintain(args = []) {
+    const dryRun = args.includes("--dry-run");
+    const phrenPath = getPhrenPath();
+    const { execSync } = await import("child_process");
+    const report = {
+        gitGcRan: false,
+        commitsSquashed: 0,
+        sessionsRemoved: 0,
+        runtimeLogsRemoved: 0,
+    };
+    // 1. Run git gc --aggressive on the ~/.phren repo
+    if (dryRun) {
+        console.log("[dry-run] Would run: git gc --aggressive");
+    }
+    else {
+        try {
+            execSync("git gc --aggressive --quiet", { cwd: phrenPath, stdio: "pipe" });
+            report.gitGcRan = true;
+            console.log("git gc --aggressive: done");
+        }
+        catch (err) {
+            console.error(`git gc failed: ${errorMessage(err)}`);
+        }
+    }
+    // 2. Squash old auto-save commits (older than 7 days) into weekly summaries
+    const sevenDaysAgo = new Date(Date.now() - 7 * 86400000).toISOString().slice(0, 10);
+    let oldCommits = [];
+    try {
+        const raw = execSync(`git log --oneline --before="${sevenDaysAgo}" --format="%H %s"`, { cwd: phrenPath, encoding: "utf8" }).trim();
+        if (raw) {
+            oldCommits = raw.split("\n").filter((l) => l.includes("auto-save:") || l.includes("[auto]"));
+        }
+    }
+    catch {
+        // Not a git repo or no commits — skip silently
+    }
+    if (oldCommits.length === 0) {
+        console.log("Commit squash: no old auto-save commits to squash.");
+    }
+    else if (dryRun) {
+        console.log(`[dry-run] Would squash ${oldCommits.length} auto-save commits older than 7 days into weekly summaries.`);
+        report.commitsSquashed = oldCommits.length;
+    }
+    else {
+        // Group by ISO week (YYYY-Www) based on commit timestamp
+        const commitsByWeek = new Map();
+        for (const line of oldCommits) {
+            const hash = line.split(" ")[0];
+            try {
+                const dateStr = execSync(`git log -1 --format="%ci" ${hash}`, { cwd: phrenPath, encoding: "utf8" }).trim();
+                const date = new Date(dateStr);
+                const weekStart = new Date(date);
+                weekStart.setDate(date.getDate() - date.getDay()); // start of week (Sunday)
+                const weekKey = weekStart.toISOString().slice(0, 10);
+                if (!commitsByWeek.has(weekKey))
+                    commitsByWeek.set(weekKey, []);
+                commitsByWeek.get(weekKey).push(hash);
+            }
+            catch {
+                // Skip commits we can't resolve
+            }
+        }
+        // For each week with multiple commits, soft-reset to oldest and amend into a summary
+        for (const [weekKey, hashes] of commitsByWeek.entries()) {
+            if (hashes.length < 2)
+                continue;
+            try {
+                const oldest = hashes[hashes.length - 1];
+                const newest = hashes[0];
+                // Use git rebase --onto to squash: squash all into the oldest parent
+                const parentOfOldest = execSync(`git rev-parse ${oldest}^`, { cwd: phrenPath, encoding: "utf8" }).trim();
+                // Build rebase script via env variable to squash all but first to "squash"
+                const rebaseScript = hashes
+                    .map((h, i) => `${i === hashes.length - 1 ? "pick" : "squash"} ${h} auto-save`)
+                    .reverse()
+                    .join("\n");
+                const scriptPath = path.join(phrenPath, ".runtime", `gc-rebase-${weekKey}.sh`);
+                fs.writeFileSync(scriptPath, rebaseScript);
+                // Use GIT_SEQUENCE_EDITOR to feed our script
+                execSync(`GIT_SEQUENCE_EDITOR="cat ${scriptPath} >" git rebase -i ${parentOfOldest}`, { cwd: phrenPath, stdio: "pipe" });
+                fs.unlinkSync(scriptPath);
+                report.commitsSquashed += hashes.length - 1;
+                console.log(`Squashed ${hashes.length} auto-save commits for week of ${weekKey} (${newest.slice(0, 7)}..${oldest.slice(0, 7)}).`);
+            }
+            catch {
+                // Squashing is best-effort — log and continue
+                console.warn(`  Could not squash auto-save commits for week ${weekKey} (possibly non-linear history). Skipping.`);
+            }
+        }
+        if (report.commitsSquashed === 0) {
+            console.log("Commit squash: all old auto-save weeks have only one commit, nothing to squash.");
+        }
+    }
+    // 3. Prune stale session markers from ~/.phren/.sessions/ older than 30 days
+    const sessionsDir = path.join(phrenPath, ".sessions");
+    const thirtyDaysAgo = Date.now() - 30 * 86400000;
+    if (fs.existsSync(sessionsDir)) {
+        const entries = fs.readdirSync(sessionsDir);
+        for (const entry of entries) {
+            const fullPath = path.join(sessionsDir, entry);
+            try {
+                const stat = fs.statSync(fullPath);
+                if (stat.mtimeMs < thirtyDaysAgo) {
+                    if (dryRun) {
+                        console.log(`[dry-run] Would remove session marker: .sessions/${entry}`);
+                    }
+                    else {
+                        fs.unlinkSync(fullPath);
+                    }
+                    report.sessionsRemoved++;
+                }
+            }
+            catch {
+                // Skip unreadable entries
+            }
+        }
+    }
+    const sessionsVerb = dryRun ? "Would remove" : "Removed";
+    console.log(`${sessionsVerb} ${report.sessionsRemoved} stale session marker(s) from .sessions/`);
+    // 4. Trim runtime logs from ~/.phren/.runtime/ older than 30 days
+    const runtimeDir = path.join(phrenPath, ".runtime");
+    const logExtensions = new Set([".log", ".jsonl", ".json"]);
+    if (fs.existsSync(runtimeDir)) {
+        const entries = fs.readdirSync(runtimeDir);
+        for (const entry of entries) {
+            const ext = path.extname(entry);
+            if (!logExtensions.has(ext))
+                continue;
+            // Never trim the active audit log or telemetry config
+            if (entry === "audit.log" || entry === "telemetry.json")
+                continue;
+            const fullPath = path.join(runtimeDir, entry);
+            try {
+                const stat = fs.statSync(fullPath);
+                if (stat.mtimeMs < thirtyDaysAgo) {
+                    if (dryRun) {
+                        console.log(`[dry-run] Would remove runtime log: .runtime/${entry}`);
+                    }
+                    else {
+                        fs.unlinkSync(fullPath);
+                    }
+                    report.runtimeLogsRemoved++;
+                }
+            }
+            catch {
+                // Skip unreadable entries
+            }
+        }
+    }
+    const logsVerb = dryRun ? "Would remove" : "Removed";
+    console.log(`${logsVerb} ${report.runtimeLogsRemoved} stale runtime log(s) from .runtime/`);
+    // 5. Summary
+    if (!dryRun) {
+        appendAuditLog(phrenPath, "maintain_gc", `gitGc=${report.gitGcRan} squashed=${report.commitsSquashed} sessions=${report.sessionsRemoved} logs=${report.runtimeLogsRemoved}`);
+    }
+    console.log(`\nGC complete:${dryRun ? " (dry-run)" : ""}` +
+        ` git_gc=${report.gitGcRan}` +
+        ` commits_squashed=${report.commitsSquashed}` +
+        ` sessions_pruned=${report.sessionsRemoved}` +
+        ` logs_pruned=${report.runtimeLogsRemoved}`);
+}
 // ── Maintain router ──────────────────────────────────────────────────────────
 export async function handleMaintain(args) {
     const sub = args[0];
@@ -245,6 +406,8 @@ export async function handleMaintain(args) {
             return handleExtractMemories(rest[0]);
         case "restore":
             return handleRestoreBackup(rest);
+        case "gc":
+            return handleGcMaintain(rest);
         default:
             console.log(`phren maintain - memory maintenance and governance
 
@@ -258,7 +421,9 @@ Subcommands:
                                          Deduplicate FINDINGS.md bullets. Run after a burst of work
                                          when findings feel repetitive, or monthly to keep things clean.
   phren maintain extract [project]      Mine git/GitHub signals into memory candidates
-  phren maintain restore [project]      List and restore from .bak files`);
+  phren maintain restore [project]      List and restore from .bak files
+  phren maintain gc [--dry-run]         Garbage-collect the ~/.phren repo: git gc, squash old
+                                         auto-save commits, prune stale session markers and runtime logs`);
             if (sub) {
                 console.error(`\nUnknown maintain subcommand: "${sub}"`);
                 process.exit(1);

package/mcp/dist/cli-hooks.js

@@ -345,7 +345,7 @@ export async function handleHookPrompt() {
                 parts.push(`Findings ready for consolidation:`);
                 parts.push(notices.join("\n"));
                 parts.push(`Run phren-consolidate when ready.`);
-                parts.push(`</phren-notice>`);
+                parts.push(`<phren-notice>`);
             }
             if (noticeFile) {
                 try {
@@ -367,7 +367,7 @@ export async function handleHookPrompt() {
     }
     catch (err) {
         const msg = errorMessage(err);
-        process.stdout.write(`\n<phren-error>phren hook failed: ${msg}. Check ~/.phren/.runtime/debug.log for details.</phren-error>\n`);
+        process.stdout.write(`\n<phren-error>phren hook failed: ${msg}. Check ~/.phren/.runtime/debug.log for details.<phren-error>\n`);
         debugLog(`hook-prompt error: ${msg}`);
         process.exit(0);
     }

package/mcp/dist/content-citation.js

@@ -5,7 +5,7 @@ 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, parseFindingLifecycle } from "./finding-lifecycle.js";
+import { FINDING_TYPE_DECAY, extractFindingType } from "./finding-lifecycle.js";
 export const FINDING_PROVENANCE_SOURCES = [
     "human",
     "agent",
@@ -294,7 +294,6 @@ export function filterTrustedFindingsDetailed(content, opts) {
         ...(options.decay || {}),
     };
     const highImpactFindingIds = options.highImpactFindingIds;
-    const impactCounts = options.impactCounts;
     const project = options.project;
     const lines = content.split("\n");
     const out = [];
@@ -413,29 +412,20 @@ export function filterTrustedFindingsDetailed(content, opts) {
             confidence *= 0.9;
         if (project && highImpactFindingIds?.size) {
             const findingId = findingIdFromLine(line);
-            if (highImpactFindingIds.has(findingId)) {
-                // Get surface count for graduated boost
-                const surfaceCount = impactCounts?.get(findingId) ?? 3;
-                // Log-scaled: 3→1.15x, 10→1.28x, 30→1.38x, capped at 1.4x
-                const boost = Math.min(1.4, 1 + 0.1 * Math.log2(Math.max(3, surfaceCount)));
-                confidence *= boost;
-                // Decay resistance: confirmed findings decay 3x slower
-                if (effectiveDate) {
-                    const realAge = ageDaysForDate(effectiveDate);
-                    if (realAge !== null) {
-                        const slowedAge = Math.floor(realAge / 3);
-                        confidence = Math.max(confidence, confidenceForAge(slowedAge, decay));
-                    }
+            if (highImpactFindingIds.has(findingId))
+                confidence *= 1.15;
+        }
+        // Confirmed findings decay 3x slower — recompute confidence with reduced age
+        {
+            const findingId = findingIdFromLine(line);
+            if (findingId && highImpactFindingIds?.has(findingId) && effectiveDate) {
+                const realAge = ageDaysForDate(effectiveDate);
+                if (realAge !== null) {
+                    const slowedAge = Math.floor(realAge / 3);
+                    confidence = Math.max(confidence, confidenceForAge(slowedAge, decay));
                 }
             }
         }
-        const lifecycle = parseFindingLifecycle(line);
-        if (lifecycle?.status === "superseded")
-            confidence *= 0.25;
-        if (lifecycle?.status === "retracted")
-            confidence *= 0.1;
-        if (lifecycle?.status === "contradicted")
-            confidence *= 0.4;
         confidence = Math.max(0, Math.min(1, confidence));
         if (confidence < minConfidence) {
             issues.push({ date: effectiveDate || "unknown", bullet: line, reason: "stale" });

package/mcp/dist/data-access.js

@@ -8,7 +8,7 @@ import { isValidProjectName, queueFilePath, safeProjectPath, errorMessage } from
 import { parseCitationComment, parseSourceComment, } from "./content-citation.js";
 import { parseFindingLifecycle, } from "./finding-lifecycle.js";
 import { METADATA_REGEX, isCitationLine, isArchiveStart, isArchiveEnd, parseFindingId, parseAllContradictions, stripComments, } from "./content-metadata.js";
-export { readTasks, readTasksAcrossProjects, resolveTaskItem, addTask, addTasks, completeTasks, completeTask, removeTask, updateTask, linkTaskIssue, pinTask, unpinTask, workNextTask, tidyDoneTasks, taskMarkdown, appendChildFinding, promoteTask, TASKS_FILENAME, TASK_FILE_ALIASES, canonicalTaskFilePath, resolveTaskFilePath, isTaskFileName, } from "./data-tasks.js";
+export { readTasks, readTasksAcrossProjects, resolveTaskItem, addTask, addTasks, completeTasks, completeTask, removeTask, removeTasks, updateTask, linkTaskIssue, pinTask, unpinTask, workNextTask, tidyDoneTasks, taskMarkdown, appendChildFinding, promoteTask, TASKS_FILENAME, TASK_FILE_ALIASES, canonicalTaskFilePath, resolveTaskFilePath, isTaskFileName, } from "./data-tasks.js";
 export { addProjectToProfile, listMachines, listProfiles, listProjectCards, removeProjectFromProfile, setMachineProfile, } from "./profile-store.js";
 export { loadShellState, readRuntimeHealth, resetShellState, saveShellState, } from "./shell-state-store.js";
 function withSafeLock(filePath, fn) {

package/mcp/dist/data-tasks.js

@@ -528,6 +528,29 @@ export function removeTask(phrenPath, project, match) {
         return phrenOk(`Removed task from ${project}: ${item.line}`);
     });
 }
+export function removeTasks(phrenPath, project, matches) {
+    const bPath = canonicalTaskFilePath(phrenPath, project);
+    if (!bPath)
+        return phrenErr(`Project name "${project}" is not valid.`, PhrenError.INVALID_PROJECT_NAME);
+    return withSafeLock(bPath, () => {
+        const parsed = readTasks(phrenPath, project);
+        if (!parsed.ok)
+            return forwardErr(parsed);
+        const removed = [];
+        const errors = [];
+        for (const match of matches) {
+            const found = findItemByMatch(parsed.data, match);
+            if (found.error || !found.match) {
+                errors.push(match);
+                continue;
+            }
+            const [item] = parsed.data.items[found.match.section].splice(found.match.index, 1);
+            removed.push(item.line);
+        }
+        writeTaskDoc(parsed.data);
+        return phrenOk({ removed, errors });
+    });
+}
 export function updateTask(phrenPath, project, match, updates) {
     const bPath = canonicalTaskFilePath(phrenPath, project);
     if (!bPath)

package/mcp/dist/mcp-tasks.js

@@ -3,7 +3,7 @@ import { z } from "zod";
 import * as fs from "fs";
 import * as path from "path";
 import { isValidProjectName } from "./utils.js";
-import { addTask as addTaskStore, addTasks as addTasksBatch, taskMarkdown, completeTask as completeTaskStore, completeTasks as completeTasksBatch, removeTask as removeTaskStore, linkTaskIssue, pinTask, workNextTask, tidyDoneTasks, readTasks, readTasksAcrossProjects, resolveTaskItem, TASKS_FILENAME, updateTask as updateTaskStore, promoteTask, } from "./data-access.js";
+import { addTask as addTaskStore, addTasks as addTasksBatch, taskMarkdown, completeTask as completeTaskStore, completeTasks as completeTasksBatch, removeTask as removeTaskStore, removeTasks as removeTasksBatch, linkTaskIssue, pinTask, workNextTask, tidyDoneTasks, readTasks, readTasksAcrossProjects, resolveTaskItem, TASKS_FILENAME, updateTask as updateTaskStore, promoteTask, } from "./data-access.js";
 import { applyGravity } from "./data-tasks.js";
 import { buildTaskIssueBody, createGithubIssueForTask, parseGithubIssueUrl, resolveProjectGithubRepo, } from "./tasks-github.js";
 import { clearTaskCheckpoint } from "./session-checkpoints.js";
@@ -327,6 +327,26 @@ export function register(server, ctx) {
             return mcpResponse({ ok: true, message: result.data, data: { project, item } });
         });
     });
+    server.registerTool("remove_tasks", {
+        title: "◆ phren · remove tasks (bulk)",
+        description: "Remove multiple tasks in one call. Pass an array of partial item texts or IDs.",
+        inputSchema: z.object({
+            project: z.string().describe("Project name."),
+            items: z.array(z.string()).describe("List of partial item texts or IDs to remove."),
+        }),
+    }, async ({ project, items }) => {
+        if (!isValidProjectName(project))
+            return mcpResponse({ ok: false, error: `Invalid project name: "${project}"` });
+        return withWriteQueue(async () => {
+            const result = removeTasksBatch(phrenPath, project, items);
+            if (!result.ok)
+                return mcpResponse({ ok: false, error: result.error });
+            const { removed, errors } = result.data;
+            if (removed.length > 0)
+                refreshTaskIndex(updateFileInIndex, phrenPath, project);
+            return mcpResponse({ ok: removed.length > 0, ...(removed.length === 0 ? { error: `No tasks removed: ${errors.join("; ")}` } : {}), message: `Removed ${removed.length}/${items.length} items`, data: { project, removed, errors } });
+        });
+    });
     server.registerTool("update_task", {
         title: "◆ phren · update task",
         description: "Update a task's text, priority, context, section, or GitHub metadata by matching text.",

package/mcp/dist/shared-retrieval.js

@@ -3,7 +3,7 @@ import { getQualityMultiplier, entryScoreKey, } from "./shared-governance.js";
 import { queryDocRows, queryRows, cosineFallback, extractSnippet, getDocSourceKey, getEntityBoostDocs, decodeFiniteNumber, rowToDocWithRowid, } from "./shared-index.js";
 import { filterTrustedFindingsDetailed, } from "./shared-content.js";
 import { parseCitationComment } from "./content-citation.js";
-import { getHighImpactFindings, getImpactSurfaceCounts } from "./finding-impact.js";
+import { getHighImpactFindings } from "./finding-impact.js";
 import { buildFtsQueryVariants, buildRelaxedFtsQuery, isFeatureEnabled, STOP_WORDS } from "./utils.js";
 import * as fs from "fs";
 import * as path from "path";
@@ -36,7 +36,7 @@ const LOW_VALUE_BULLET_FRACTION = 0.5;
 // ── Intent and scoring helpers ───────────────────────────────────────────────
 export function detectTaskIntent(prompt) {
     const p = prompt.toLowerCase();
-    if (/(^|\s)\/[a-z][a-z0-9_-]{1,63}(?=$|\s|[.,:;!?])/.test(p) || /\b(skill|swarm|lineup|slash command)\b/.test(p))
+    if (/(?:^|\s)\/(?!(?:home|usr|var|tmp|etc|opt|api|mnt)\b)[a-z][\w-]*\b/.test(p) || /\bskill\b/.test(p))
         return "skill";
     if (/(bug|error|fix|broken|regression|fail|stack trace)/.test(p))
         return "debug";
@@ -49,8 +49,6 @@ export function detectTaskIntent(prompt) {
     return "general";
 }
 function intentBoost(intent, docType) {
-    if (intent === "skill" && docType === "skill")
-        return 4;
     if (intent === "debug" && (docType === "findings" || docType === "reference"))
         return 3;
     if (intent === "review" && (docType === "canonical" || docType === "changelog"))
@@ -347,23 +345,10 @@ export function searchDocuments(db, safeQuery, prompt, keywords, detectedProject
     if (ftsDocs.length === 0 && relaxedQuery && relaxedQuery !== safeQuery) {
         runScopedFtsQuery(relaxedQuery);
     }
-    // Tier 1.5: Fragment graph expansion
-    const fragmentExpansionDocs = [];
-    const queryLower = (prompt + " " + keywords).toLowerCase();
-    const fragmentBoostDocKeys = getEntityBoostDocs(db, queryLower);
-    for (const docKey of fragmentBoostDocKeys) {
-        if (ftsSeenKeys.has(docKey))
-            continue;
-        const rows = queryDocRows(db, "SELECT project, filename, type, content, path FROM docs WHERE path = ? LIMIT 1", [docKey]);
-        if (rows?.length) {
-            ftsSeenKeys.add(docKey);
-            fragmentExpansionDocs.push(rows[0]);
-        }
-    }
     // Tier 2: Token-overlap semantic — always run, scored independently
     const semanticDocs = semanticFallbackDocs(db, `${prompt}\n${keywords}`, detectedProject);
     // Merge with Reciprocal Rank Fusion so documents found by both tiers rank highest
-    const merged = rrfMerge([ftsDocs, fragmentExpansionDocs, semanticDocs]);
+    const merged = rrfMerge([ftsDocs, semanticDocs]);
     if (merged.length === 0)
         return null;
     return merged.slice(0, 12);
@@ -400,7 +385,7 @@ export async function searchDocumentsAsync(db, safeQuery, prompt, keywords, dete
     }
     catch (err) {
         // Vector search failure is non-fatal — return sync result
-        if (process.env.PHREN_DEBUG)
+        if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG))
             process.stderr.write(`[phren] hybridSearch vectorFallback: ${err instanceof Error ? err.message : String(err)}\n`);
         return syncResult;
     }
@@ -500,7 +485,7 @@ export async function searchKnowledgeRows(db, options) {
             }
         }
         catch (err) {
-            if (process.env.PHREN_DEBUG) {
+            if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG)) {
                 process.stderr.write(`[phren] vectorFallback: ${err instanceof Error ? err.message : String(err)}\n`);
             }
         }
@@ -515,7 +500,6 @@ export function applyTrustFilter(rows, ttlDays, minConfidence, decay, phrenPath)
     const queueItems = [];
     const auditEntries = [];
     const highImpactFindingIds = phrenPath ? getHighImpactFindings(phrenPath, 3) : undefined;
-    const impactCounts = phrenPath ? getImpactSurfaceCounts(phrenPath, 1) : undefined;
     const filtered = rows
         .map((doc) => {
         if (!TRUST_FILTERED_TYPES.has(doc.type))
@@ -526,7 +510,6 @@ export function applyTrustFilter(rows, ttlDays, minConfidence, decay, phrenPath)
             decay,
             project: doc.project,
             highImpactFindingIds,
-            impactCounts,
         });
         if (trust.issues.length > 0) {
             const stale = trust.issues.filter((i) => i.reason === "stale").map((i) => i.bullet);
@@ -630,7 +613,7 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
     const scored = ranked.map((doc) => {
         const globBoost = getProjectGlobBoost(phrenPathLocal, doc.project, cwd, gitCtx?.changedFiles);
         const key = entryScoreKey(doc.project, doc.filename, doc.content);
-        const entity = entityBoostPaths.has(doc.path) ? 1.5 : 1;
+        const entity = entityBoostPaths.has(doc.path) ? 1.3 : 1;
         const date = getRecentDate(doc);
         const fileRel = fileRelevanceBoost(doc.path, changedFiles);
         const branchMat = branchMatchBoost(doc.content, gitCtx?.branch);
@@ -645,12 +628,7 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
             && queryOverlap < WEAK_CROSS_PROJECT_OVERLAP_MAX
             ? WEAK_CROSS_PROJECT_OVERLAP_PENALTY
             : 0;
-        // Boost skills whose filename matches a query token (e.g. "swarm" matches swarm.md)
-        const skillNameBoost = doc.type === "skill" && queryTokens.length > 0
-            ? queryTokens.some((t) => doc.filename.replace(/\.md$/i, "").toLowerCase() === t) ? 4 : 0
-            : 0;
         const score = Math.round((intentBoost(intent, doc.type) +
-            skillNameBoost +
             fileRel +
             branchMat +
             globBoost +
@@ -754,7 +732,7 @@ export function markStaleCitations(snippet) {
                             }
                         }
                         catch (err) {
-                            if (process.env.PHREN_DEBUG)
+                            if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG))
                                 process.stderr.write(`[phren] applyCitationAnnotations fileRead: ${err instanceof Error ? err.message : String(err)}\n`);
                             stale = true;
                         }
@@ -771,23 +749,6 @@ export function markStaleCitations(snippet) {
     }
     return result.join("\n");
 }
-function annotateContradictions(snippet) {
-    return snippet.split('\n').map(line => {
-        const conflictMatch = line.match(/<!-- conflicts_with: "(.*?)" -->/);
-        const contradictMatch = line.match(/<!-- phren:contradicts "(.*?)" -->/);
-        const statusMatch = line.match(/phren:status "contradicted"/);
-        if (conflictMatch) {
-            return line.replace(conflictMatch[0], '') + ` [CONTRADICTED — conflicts with: "${conflictMatch[1]}"]`;
-        }
-        if (contradictMatch) {
-            return line.replace(contradictMatch[0], '') + ` [CONTRADICTED — see: "${contradictMatch[1]}"]`;
-        }
-        if (statusMatch) {
-            return line + ' [CONTRADICTED]';
-        }
-        return line;
-    }).join('\n');
-}
 export function selectSnippets(rows, keywords, tokenBudget, lineBudget, charBudget) {
     const selected = [];
     let usedTokens = 36;
@@ -813,7 +774,6 @@ export function selectSnippets(rows, keywords, tokenBudget, lineBudget, charBudg
         if (TRUST_FILTERED_TYPES.has(doc.type)) {
             snippet = markStaleCitations(snippet);
         }
-        snippet = annotateContradictions(snippet);
         snippet = dedupSnippetBullets(snippet);
         if (!snippet.trim())
             continue;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.0.9",
+  "version": "0.0.10",
   "description": "Knowledge layer for AI agents. Claude remembers you. Phren remembers your work.",
   "type": "module",
   "bin": {