@phren/cli 0.0.5 → 0.0.7

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 } from "./finding-impact.js";
+import { getHighImpactFindings, getImpactSurfaceCounts } from "./finding-impact.js";
 import { buildFtsQueryVariants, buildRelaxedFtsQuery, isFeatureEnabled, STOP_WORDS } from "./utils.js";
 import * as fs from "fs";
 import * as path from "path";
@@ -12,7 +12,6 @@ import { vectorFallback } from "./shared-search-fallback.js";
 import { getOllamaUrl, getCloudEmbeddingUrl } from "./shared-ollama.js";
 import { keywordFallbackSearch } from "./core-search.js";
 import { debugLog } from "./shared.js";
-import { getCorrelatedDocs } from "./query-correlation.js";
 // ── Scoring constants ─────────────────────────────────────────────────────────
 /** Number of docs sampled for token-overlap semantic fallback search. */
 const SEMANTIC_FALLBACK_SAMPLE_LIMIT = 100;
@@ -32,13 +31,13 @@ const LOW_FOCUS_SNIPPET_CHAR_FRACTION = 0.55;
 const TASK_RESCUE_MIN_OVERLAP = 0.3;
 const TASK_RESCUE_OVERLAP_MARGIN = 0.12;
 const TASK_RESCUE_SCORE_MARGIN = 0.6;
-/** Boost applied to docs that correlate with recurring query patterns. */
-const CORRELATION_BOOST = 1.5;
 /** Fraction of bullets that must be low-value before applying the low-value penalty. */
 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}(?=$|\s|[.,:;!?])/.test(p) || /\b(skill|swarm|lineup|slash command)\b/.test(p))
+        return "skill";
     if (/(bug|error|fix|broken|regression|fail|stack trace)/.test(p))
         return "debug";
     if (/(review|audit|pr|pull request|nit|refactor)/.test(p))
@@ -50,6 +49,8 @@ export function detectTaskIntent(prompt) {
     return "general";
 }
 function intentBoost(intent, docType) {
+    if (intent === "skill" && docType === "skill")
+        return 4;
     if (intent === "debug" && (docType === "findings" || docType === "reference"))
         return 3;
     if (intent === "review" && (docType === "canonical" || docType === "changelog"))
@@ -346,10 +347,23 @@ export function searchDocuments(db, safeQuery, prompt, keywords, detectedProject
     if (ftsDocs.length === 0 && relaxedQuery && relaxedQuery !== safeQuery) {
         runScopedFtsQuery(relaxedQuery);
     }
+    // Tier 1.5: Fragment graph expansion
+    const fragmentExpansionDocs = [];
+    const queryLower = (prompt + " " + keywords).toLowerCase();
+    const fragmentBoostDocKeys = getEntityBoostDocs(db, queryLower);
+    for (const docKey of fragmentBoostDocKeys) {
+        if (ftsSeenKeys.has(docKey))
+            continue;
+        const rows = queryDocRows(db, "SELECT project, filename, type, content, path FROM docs WHERE path = ? LIMIT 1", [docKey]);
+        if (rows?.length) {
+            ftsSeenKeys.add(docKey);
+            fragmentExpansionDocs.push(rows[0]);
+        }
+    }
     // Tier 2: Token-overlap semantic — always run, scored independently
     const semanticDocs = semanticFallbackDocs(db, `${prompt}\n${keywords}`, detectedProject);
     // Merge with Reciprocal Rank Fusion so documents found by both tiers rank highest
-    const merged = rrfMerge([ftsDocs, semanticDocs]);
+    const merged = rrfMerge([ftsDocs, fragmentExpansionDocs, semanticDocs]);
     if (merged.length === 0)
         return null;
     return merged.slice(0, 12);
@@ -386,7 +400,7 @@ 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 || process.env.PHREN_DEBUG))
+        if (process.env.PHREN_DEBUG)
             process.stderr.write(`[phren] hybridSearch vectorFallback: ${err instanceof Error ? err.message : String(err)}\n`);
         return syncResult;
     }
@@ -486,7 +500,7 @@ export async function searchKnowledgeRows(db, options) {
             }
         }
         catch (err) {
-            if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG)) {
+            if (process.env.PHREN_DEBUG) {
                 process.stderr.write(`[phren] vectorFallback: ${err instanceof Error ? err.message : String(err)}\n`);
             }
         }
@@ -501,6 +515,7 @@ export function applyTrustFilter(rows, ttlDays, minConfidence, decay, phrenPath)
     const queueItems = [];
     const auditEntries = [];
     const highImpactFindingIds = phrenPath ? getHighImpactFindings(phrenPath, 3) : undefined;
+    const impactCounts = phrenPath ? getImpactSurfaceCounts(phrenPath, 1) : undefined;
     const filtered = rows
         .map((doc) => {
         if (!TRUST_FILTERED_TYPES.has(doc.type))
@@ -511,6 +526,7 @@ export function applyTrustFilter(rows, ttlDays, minConfidence, decay, phrenPath)
             decay,
             project: doc.project,
             highImpactFindingIds,
+            impactCounts,
         });
         if (trust.issues.length > 0) {
             const stale = trust.issues.filter((i) => i.reason === "stale").map((i) => i.bullet);
@@ -608,15 +624,13 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
         }
     }
     const getRecentDate = (doc) => recentDateCache.get(doc.path || `${doc.project}/${doc.filename}`) ?? "0000-00-00";
-    // Query correlation: pre-warm docs that historically correlated with similar queries
-    const correlatedDocKeys = query ? new Set(getCorrelatedDocs(phrenPathLocal, query, 5)) : new Set();
     // Precompute per-doc ranking metadata once — avoids recomputing inside sort comparator.
     const changedFiles = gitCtx?.changedFiles || new Set();
     const FILE_MATCH_BOOST = 1.5;
     const scored = ranked.map((doc) => {
         const globBoost = getProjectGlobBoost(phrenPathLocal, doc.project, cwd, gitCtx?.changedFiles);
         const key = entryScoreKey(doc.project, doc.filename, doc.content);
-        const entity = entityBoostPaths.has(doc.path) ? 1.3 : 1;
+        const entity = entityBoostPaths.has(doc.path) ? 1.5 : 1;
         const date = getRecentDate(doc);
         const fileRel = fileRelevanceBoost(doc.path, changedFiles);
         const branchMat = branchMatchBoost(doc.content, gitCtx?.branch);
@@ -631,17 +645,19 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
             && queryOverlap < WEAK_CROSS_PROJECT_OVERLAP_MAX
             ? WEAK_CROSS_PROJECT_OVERLAP_PENALTY
             : 0;
-        const correlationKey = `${doc.project}/${doc.filename}`;
-        const correlationBoost = correlatedDocKeys.has(correlationKey) ? CORRELATION_BOOST : 0;
+        // Boost skills whose filename matches a query token (e.g. "swarm" matches swarm.md)
+        const skillNameBoost = doc.type === "skill" && queryTokens.length > 0
+            ? queryTokens.some((t) => doc.filename.replace(/\.md$/i, "").toLowerCase() === t) ? 4 : 0
+            : 0;
         const score = Math.round((intentBoost(intent, doc.type) +
+            skillNameBoost +
             fileRel +
             branchMat +
             globBoost +
             qualityMult +
             entity +
             queryOverlap * queryOverlapWeight +
-            recencyBoost(doc.type, date) +
-            correlationBoost -
+            recencyBoost(doc.type, date) -
             weakCrossProjectPenalty -
             lowValuePenalty(doc.content, doc.type)) * crossProjectAgeMultiplier(doc, detectedProject, date) * 10000) / 10000;
         const fileMatch = fileRel > 0 || branchMat > 0;
@@ -706,24 +722,6 @@ export function rankResults(rows, intent, gitCtx, detectedProject, phrenPathLoca
     }
     return ranked;
 }
-/** Annotate snippet lines that carry contradiction metadata with visible markers. */
-export 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');
-}
 /** Mark snippet lines with stale citations (cited file missing or line content changed). */
 export function markStaleCitations(snippet) {
     const lines = snippet.split("\n");
@@ -756,7 +754,7 @@ export function markStaleCitations(snippet) {
                             }
                         }
                         catch (err) {
-                            if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG))
+                            if (process.env.PHREN_DEBUG)
                                 process.stderr.write(`[phren] applyCitationAnnotations fileRead: ${err instanceof Error ? err.message : String(err)}\n`);
                             stale = true;
                         }
@@ -773,10 +771,40 @@ export function markStaleCitations(snippet) {
     }
     return result.join("\n");
 }
+function annotateContradictions(snippet) {
+    return snippet.split('\n').map(line => {
+        const conflictMatch = line.match(/<!-- conflicts_with: "(.*?)" -->/);
+        const contradictMatch = line.match(/<!-- phren:contradicts "(.*?)" -->/);
+        const statusMatch = line.match(/phren:status "contradicted"/);
+        if (conflictMatch) {
+            return line.replace(conflictMatch[0], '') + ` [CONTRADICTED — conflicts with: "${conflictMatch[1]}"]`;
+        }
+        if (contradictMatch) {
+            return line.replace(contradictMatch[0], '') + ` [CONTRADICTED — see: "${contradictMatch[1]}"]`;
+        }
+        if (statusMatch) {
+            return line + ' [CONTRADICTED]';
+        }
+        return line;
+    }).join('\n');
+}
 export function selectSnippets(rows, keywords, tokenBudget, lineBudget, charBudget) {
     const selected = [];
     let usedTokens = 36;
     const queryTokens = tokenizeForOverlap(keywords);
+    const seenBullets = new Set();
+    // For each snippet being added, hash its bullet lines and skip duplicates
+    function dedupSnippetBullets(snippet) {
+        return snippet.split('\n').filter(line => {
+            if (!line.startsWith('- '))
+                return true; // Keep non-bullet lines (headers, etc)
+            const normalized = line.replace(/<!--.*?-->/g, '').trim().toLowerCase();
+            if (seenBullets.has(normalized))
+                return false;
+            seenBullets.add(normalized);
+            return true;
+        }).join('\n');
+    }
     for (const doc of rows) {
         let snippet = compactSnippet(extractSnippet(doc.content, keywords, 8), lineBudget, charBudget);
         if (!snippet.trim())
@@ -785,8 +813,10 @@ export function selectSnippets(rows, keywords, tokenBudget, lineBudget, charBudg
         if (TRUST_FILTERED_TYPES.has(doc.type)) {
             snippet = markStaleCitations(snippet);
         }
-        // Surface contradiction metadata as visible annotations
         snippet = annotateContradictions(snippet);
+        snippet = dedupSnippetBullets(snippet);
+        if (!snippet.trim())
+            continue;
         let focusScore = queryTokens.length > 0
             ? overlapScore(queryTokens, `${doc.filename}\n${snippet}`)
             : 1;

package/mcp/dist/shared.js

@@ -1,7 +1,7 @@
 import * as fs from "fs";
 import * as path from "path";
 import { debugLog, runtimeFile } from "./phren-paths.js";
-import { errorMessage, isValidProjectName } from "./utils.js";
+import { errorMessage } from "./utils.js";
 export { HOOK_TOOL_NAMES, hookConfigPath } from "./provider-adapters.js";
 export { EXEC_TIMEOUT_MS, EXEC_TIMEOUT_QUICK_MS, PhrenError, phrenOk, phrenErr, forwardErr, parsePhrenErrorCode, isRecord, withDefaults, FINDING_TYPES, FINDING_TAGS, KNOWN_OBSERVATION_TAGS, DOC_TYPES, capCache, } from "./phren-core.js";
 export { ROOT_MANIFEST_FILENAME, homeDir, homePath, expandHomePath, defaultPhrenPath, rootManifestPath, readRootManifest, writeRootManifest, resolveInstallContext, findNearestPhrenPath, isProjectLocalMode, runtimeDir, tryUnlink, sessionsDir, runtimeFile, installPreferencesFile, runtimeHealthFile, shellStateFile, sessionMetricsFile, memoryScoresFile, memoryUsageLogFile, sessionMarker, debugLog, appendIndexEvent, resolveFindingsPath, findPhrenPath, ensurePhrenPath, findPhrenPathWithArg, normalizeProjectNameForCreate, findProjectNameCaseInsensitive, getProjectDirs, collectNativeMemoryFiles, computePhrenLiveStateToken, getPhrenPath, qualityMarkers, atomicWriteText, } from "./phren-paths.js";
@@ -28,15 +28,6 @@ export function isMemoryScopeVisible(itemScope, activeScope) {
 export function impactLogFile(phrenPath) {
     return runtimeFile(phrenPath, "impact.jsonl");
 }
-function isProjectDirEntry(entry) {
-    return entry.isDirectory()
-        && !entry.name.startsWith(".")
-        && !entry.name.endsWith(".archived")
-        && !RESERVED_PROJECT_DIR_NAMES.has(entry.name);
-}
-function isCanonicalProjectDirName(name) {
-    return name === name.toLowerCase() && isValidProjectName(name);
-}
 export function appendAuditLog(phrenPath, event, details) {
     const logPath = runtimeFile(phrenPath, "audit.log");
     const line = `[${new Date().toISOString()}] ${event} ${details}\n`;

package/mcp/dist/test-global-setup.js

@@ -1,10 +1,9 @@
 /**
  * Vitest globalSetup — runs once in the main process before any test workers spawn.
  *
- * Builds mcp/dist if it is missing or stale so every fork sees a complete,
- * consistent dist artifact. Running the build here (rather than inside each
- * fork via ensureCliBuilt) eliminates the race condition where one fork runs
- * `rm -rf mcp/dist` while another fork is checking fs.existsSync(CLI_PATH).
+ * Builds mcp/dist if it is missing so every fork sees a complete, consistent
+ * dist artifact before tests begin. Individual subprocess helpers can still
+ * repair a missing artifact later under a lock if some test mutates dist.
  *
  * `pretest` in package.json already calls `npm run build`, so in normal `npm test`
  * runs this is a fast no-op check. It is the safety net for:

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@phren/cli",
-  "version": "0.0.5",
+  "version": "0.0.7",
   "description": "Knowledge layer for AI agents. Claude remembers you. Phren remembers your work.",
   "type": "module",
   "bin": {
@@ -34,7 +34,7 @@
     "vitest": "^4.0.18"
   },
   "scripts": {
-    "build": "rm -rf mcp/dist && tsc -p mcp/tsconfig.json && chmod +x mcp/dist/index.js && cp mcp/src/synonyms*.json mcp/dist/",
+    "build": "node scripts/build.mjs",
     "dev": "tsx mcp/src/index.ts",
     "lint": "eslint mcp/src/ --ignore-pattern '*.test.ts'",
     "validate-docs": "bash scripts/validate-docs.sh",