refactor: clean up CLI command output and improve error message formatting

- Consolidated console.log statements in src/cli.ts for better readability.
- Enhanced error message formatting in src/core/symbol-references.ts and src/tools/search-codebase.ts for consistency.
- Streamlined conditional object construction in src/tools/search-codebase.ts for clarity.

Author: PatrickSys

src/cli.ts

@@ -51,18 +51,14 @@ function printUsage(): void {
   console.log('');
   console.log('Commands:');
   console.log('  memory <list|add|remove>           Memory CRUD');
-  console.log(
-    '  search --query <q>                 Search the indexed codebase'
-  );
+  console.log('  search --query <q>                 Search the indexed codebase');
   console.log('         [--intent explore|edit|refactor|migrate]');
   console.log('         [--limit <n>] [--lang <l>] [--framework <f>] [--layer <l>]');
   console.log('  metadata                           Project structure, frameworks, deps');
   console.log('  status                             Index state and progress');
   console.log('  reindex [--incremental] [--reason <r>]  Re-index the codebase');
   console.log('  style-guide [--query <q>] [--category <c>]  Style guide rules');
-  console.log(
-    '  patterns [--category all|di|state|testing|libraries]  Team patterns'
-  );
+  console.log('  patterns [--category all|di|state|testing|libraries]  Team patterns');
   console.log('  refs --symbol <name> [--limit <n>]  Symbol references');
   console.log('  cycles [--scope <path>]            Circular dependency detection');
   console.log('');
@@ -202,9 +198,15 @@ export async function handleCliCommand(argv: string[]): Promise<void> {
         query: flags['query'],
         ...(flags['intent'] ? { intent: flags['intent'] } : {}),
         ...(flags['limit'] ? { limit: Number(flags['limit']) } : {}),
-        ...(flags['lang'] ? { filters: { language: flags['lang'] } } : {}),
-        ...(flags['framework'] ? { filters: { framework: flags['framework'] } } : {}),
-        ...(flags['layer'] ? { filters: { layer: flags['layer'] } } : {})
+        ...(flags['lang'] || flags['framework'] || flags['layer']
+          ? {
+              filters: {
+                ...(flags['lang'] ? { language: flags['lang'] } : {}),
+                ...(flags['framework'] ? { framework: flags['framework'] } : {}),
+                ...(flags['layer'] ? { layer: flags['layer'] } : {})
+              }
+            }
+          : {})
       };
       break;
     }

src/core/symbol-references.ts

@@ -83,7 +83,8 @@ export async function findSymbolReferences(
     chunksRaw = JSON.parse(content);
   } catch (error) {
     throw new IndexCorruptedError(
-      `Keyword index missing or unreadable (rebuild required): ${error instanceof Error ? error.message : String(error)
+      `Keyword index missing or unreadable (rebuild required): ${
+        error instanceof Error ? error.message : String(error)
       }`
     );
   }

src/index.ts

@@ -20,9 +20,7 @@ import {
   Resource
 } from '@modelcontextprotocol/sdk/types.js';
 import { CodebaseIndexer } from './core/indexer.js';
-import type {
-  IndexingStats
-} from './types/index.js';
+import type { IndexingStats } from './types/index.js';
 import { analyzerRegistry } from './core/analyzer-registry.js';
 import { AngularAnalyzer } from './analyzers/angular/index.js';
 import { GenericAnalyzer } from './analyzers/generic/index.js';
@@ -34,9 +32,7 @@ import {
   KEYWORD_INDEX_FILENAME,
   VECTOR_DB_DIRNAME
 } from './constants/codebase-context.js';
-import {
-  appendMemoryFile
-} from './memory/store.js';
+import { appendMemoryFile } from './memory/store.js';
 import { handleCliCommand } from './cli.js';
 import { parseGitLogLineToMemory } from './memory/git-memory.js';
 import {
@@ -314,7 +310,8 @@ async function generateCodebaseContext(): Promise<string> {
     lines.push('# Codebase Intelligence');
     lines.push('');
     lines.push(
-      `Index: ${index.status} (${index.confidence}, ${index.action})${index.reason ? ` — ${index.reason}` : ''
+      `Index: ${index.status} (${index.confidence}, ${index.action})${
+        index.reason ? ` — ${index.reason}` : ''
       }`
     );
     lines.push('');

src/preflight/evidence-lock.ts

@@ -165,7 +165,7 @@ export function buildEvidenceLock(input: BuildEvidenceLockInput): EvidenceLock {
     stressTriggers.push('Insufficient evidence: most evidence sources are empty');
   }
 
-  // Trigger: low caller coverage 
+  // Trigger: low caller coverage
   if (
     input.impactCoverage &&
     input.impactCoverage.total > 3 &&
@@ -214,9 +214,7 @@ export function buildEvidenceLock(input: BuildEvidenceLockInput): EvidenceLock {
   if (!readyToEdit) {
     // Code evidence weak/missing
     if (codeStrength === 'weak' || codeStrength === 'missing') {
-      whatWouldHelp.push(
-        'Search with a more specific query targeting the implementation files'
-      );
+      whatWouldHelp.push('Search with a more specific query targeting the implementation files');
     }
 
     // Pattern evidence missing

src/tools/search-codebase.ts

@@ -175,8 +175,9 @@ export async function handle(
                 text: JSON.stringify(
                   {
                     status: 'error',
-                    message: `Auto-heal retry failed: ${retryError instanceof Error ? retryError.message : String(retryError)
-                      }`
+                    message: `Auto-heal retry failed: ${
+                      retryError instanceof Error ? retryError.message : String(retryError)
+                    }`
                   },
                   null,
                   2
@@ -312,7 +313,8 @@ export async function handle(
   function buildRelationshipHints(result: SearchResult): RelationshipHints {
     const rPath = result.filePath;
     // Graph keys are relative paths with forward slashes; normalize for comparison
-    const rPathNorm = path.relative(ctx.rootPath, rPath).replace(/\\/g, '/') || rPath.replace(/\\/g, '/');
+    const rPathNorm =
+      path.relative(ctx.rootPath, rPath).replace(/\\/g, '/') || rPath.replace(/\\/g, '/');
 
     // importedBy: files that import this result (reverse lookup), collect with counts
     const importedByMap = new Map<string, number>();
@@ -394,7 +396,6 @@ export async function handle(
       const resultPaths = results.map((r) => r.filePath);
       const impactCandidates = computeImpactCandidates(resultPaths);
 
-
       // Use existing pattern intelligence for evidenceLock scoring, but keep the output payload lite.
       const preferredPatternsForEvidence: Array<{ pattern: string; example?: string }> = [];
       const patterns = intelligence.patterns || {};
@@ -410,7 +411,6 @@ export async function handle(
         }
       }
 
-
       let riskLevel: 'low' | 'medium' | 'high' = 'low';
       if (impactCandidates.length > 10) {
         riskLevel = 'high';
@@ -620,8 +620,12 @@ export async function handle(
       }
 
       // Add patterns (do/avoid, capped at 3 each, with adoption %)
-      const doPatterns = preferredPatternsForOutput.slice(0, 3).map((p) => `${p.pattern} — ${p.adoption ? ` ${p.adoption}% adoption` : ''}`);
-      const avoidPatterns = avoidPatternsForOutput.slice(0, 3).map((p) => `${p.pattern} — ${p.adoption ? ` ${p.adoption}% adoption` : ''} (declining)`);
+      const doPatterns = preferredPatternsForOutput
+        .slice(0, 3)
+        .map((p) => `${p.pattern} — ${p.adoption ? ` ${p.adoption}% adoption` : ''}`);
+      const avoidPatterns = avoidPatternsForOutput
+        .slice(0, 3)
+        .map((p) => `${p.pattern} — ${p.adoption ? ` ${p.adoption}% adoption` : ''} (declining)`);
       if (doPatterns.length > 0 || avoidPatterns.length > 0) {
         decisionCard.patterns = {
           ...(doPatterns.length > 0 && { do: doPatterns }),
@@ -720,8 +724,8 @@ export async function handle(
               confidence: searchQuality.confidence,
               ...(searchQuality.status === 'low_confidence' &&
                 searchQuality.nextSteps?.[0] && {
-                hint: searchQuality.nextSteps[0]
-              })
+                  hint: searchQuality.nextSteps[0]
+                })
             },
             ...(preflightPayload && { preflight: preflightPayload }),
             results: results.map((r) => {
@@ -737,7 +741,9 @@ export async function handle(
                 ...(r.componentType && r.layer && { type: `${r.componentType}:${r.layer}` }),
                 ...(r.trend && r.trend !== 'Stable' && { trend: r.trend }),
                 ...(r.patternWarning && { patternWarning: r.patternWarning }),
-                ...(relationshipsAndHints.relationships && { relationships: relationshipsAndHints.relationships }),
+                ...(relationshipsAndHints.relationships && {
+                  relationships: relationshipsAndHints.relationships
+                }),
                 ...(relationshipsAndHints.hints && { hints: relationshipsAndHints.hints }),
                 ...(enrichedSnippet && { snippet: enrichedSnippet })
               };