From 88afb8b47323f209eb085a527d203665070cbea1 Mon Sep 17 00:00:00 2001
From: prosdev <prosdev@users.noreply.github.com>
Date: Sat, 13 Dec 2025 19:01:06 -0800
Subject: [PATCH 1/4] fix(cli): fix dev owners subdirectory path matching

Fixed 'No ownership data found' error when running dev owners
from subdirectories like packages/.

Root cause: File paths in topFiles are absolute (from database),
but subdirectory mode was comparing them against relative paths.

Solution: Normalize absolute paths by stripping repository prefix
before comparison, matching the approach used in root directory mode.
---
 packages/cli/src/commands/owners.ts | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/packages/cli/src/commands/owners.ts b/packages/cli/src/commands/owners.ts
index 8c90c8d..de647f1 100644
--- a/packages/cli/src/commands/owners.ts
+++ b/packages/cli/src/commands/owners.ts
@@ -480,7 +480,10 @@ function formatSubdirectoryMode(
 ): string {
   // Filter developers to only those with files in current directory
   const relevantDevs = developers.filter((dev) =>
-    dev.topFiles.some((f) => f.path.startsWith(`${repositoryPath}/${currentDir}`))
+    dev.topFiles.some((f) => {
+      const relativePath = f.path.replace(`${repositoryPath}/`, '');
+      return relativePath.startsWith(currentDir);
+    })
   );
 
   if (relevantDevs.length === 0) {
@@ -498,7 +501,10 @@ function formatSubdirectoryMode(
 
   // Show top files in this directory
   const filesInDir = primary.topFiles
-    .filter((f) => f.path.startsWith(`${repositoryPath}/${currentDir}`))
+    .filter((f) => {
+      const relativePath = f.path.replace(`${repositoryPath}/`, '');
+      return relativePath.startsWith(currentDir);
+    })
     .slice(0, 5);
 
   if (filesInDir.length > 0) {

From 96fe67fbdda80fe0ed471823b18c1fb090c7c557 Mon Sep 17 00:00:00 2001
From: prosdev <prosdev@users.noreply.github.com>
Date: Sat, 13 Dec 2025 19:33:57 -0800
Subject: [PATCH 2/4] feat(cli): comprehensive indexing UX improvements

- Add update plan display to 'dev update' (shows what will change before starting)
- Add detailed progress with rates to all indexing phases (files/sec, docs/sec, commits/sec)
- Extract progress formatting to reusable updateSectionWithRate() method
- Fix NaN display when totalFiles is 0 (now shows 'Discovering...')
- Improve 'dev map' hot paths display with tree branches and file icons
- Add getUpdatePlan() public method to RepositoryIndexer

All indexing commands now show consistent detailed progress:
  1,234/4,567 files (27%, 45 files/sec)

Instead of just:
  27% complete
---
 packages/cli/src/commands/git.ts    |  8 ++-
 packages/cli/src/commands/github.ts | 10 ++--
 packages/cli/src/commands/index.ts  | 39 ++++++++-----
 packages/cli/src/commands/update.ts | 90 +++++++++++++++++++++++------
 packages/cli/src/utils/progress.ts  | 17 ++++++
 packages/core/src/indexer/index.ts  | 23 ++++++++
 packages/core/src/map/index.ts      | 36 +++++++++++-
 7 files changed, 181 insertions(+), 42 deletions(-)

diff --git a/packages/cli/src/commands/git.ts b/packages/cli/src/commands/git.ts
index 96a1894..346d07f 100644
--- a/packages/cli/src/commands/git.ts
+++ b/packages/cli/src/commands/git.ts
@@ -98,9 +98,11 @@ export const gitCommand = new Command('git')
                 }
 
                 // Update embedding progress
-                const pct = Math.round((progress.commitsProcessed / progress.totalCommits) * 100);
-                progressRenderer.updateSection(
-                  `${progress.commitsProcessed}/${progress.totalCommits} commits (${pct}%)`
+                progressRenderer.updateSectionWithRate(
+                  progress.commitsProcessed,
+                  progress.totalCommits,
+                  'commits',
+                  embeddingStartTime
                 );
               }
             },
diff --git a/packages/cli/src/commands/github.ts b/packages/cli/src/commands/github.ts
index 6d923bf..ecd703b 100644
--- a/packages/cli/src/commands/github.ts
+++ b/packages/cli/src/commands/github.ts
@@ -133,11 +133,11 @@ Related:
                 }
 
                 // Update embedding progress
-                const pct = Math.round(
-                  (progress.documentsProcessed / progress.totalDocuments) * 100
-                );
-                progressRenderer.updateSection(
-                  `${progress.documentsProcessed}/${progress.totalDocuments} documents (${pct}%)`
+                progressRenderer.updateSectionWithRate(
+                  progress.documentsProcessed,
+                  progress.totalDocuments,
+                  'documents',
+                  embeddingStartTime
                 );
               }
             },
diff --git a/packages/cli/src/commands/index.ts b/packages/cli/src/commands/index.ts
index b2144a6..3789359 100644
--- a/packages/cli/src/commands/index.ts
+++ b/packages/cli/src/commands/index.ts
@@ -199,17 +199,20 @@ export const indexCommand = new Command('index')
             }
 
             // Update embedding progress
-            const pct = Math.round((progress.documentsIndexed / progress.totalDocuments) * 100);
-            const embeddingElapsed = (Date.now() - embeddingStartTime) / 1000;
-            const docsPerSec =
-              embeddingElapsed > 0 ? progress.documentsIndexed / embeddingElapsed : 0;
-            progressRenderer.updateSection(
-              `${progress.documentsIndexed.toLocaleString()}/${progress.totalDocuments.toLocaleString()} documents (${pct}%, ${docsPerSec.toFixed(0)} docs/sec)`
+            progressRenderer.updateSectionWithRate(
+              progress.documentsIndexed,
+              progress.totalDocuments,
+              'documents',
+              embeddingStartTime
             );
           } else {
             // Scanning phase
-            const percent = progress.percentComplete || 0;
-            progressRenderer.updateSection(`${percent.toFixed(0)}% complete`);
+            progressRenderer.updateSectionWithRate(
+              progress.filesProcessed,
+              progress.totalFiles,
+              'files',
+              scanStartTime
+            );
           }
         },
       });
@@ -260,9 +263,11 @@ export const indexCommand = new Command('index')
           logger: indexLogger,
           onProgress: (progress) => {
             if (progress.phase === 'storing' && progress.totalCommits > 0) {
-              const pct = Math.round((progress.commitsProcessed / progress.totalCommits) * 100);
-              progressRenderer.updateSection(
-                `${progress.commitsProcessed}/${progress.totalCommits} commits (${pct}%)`
+              progressRenderer.updateSectionWithRate(
+                progress.commitsProcessed,
+                progress.totalCommits,
+                'commits',
+                gitStartTime
               );
             }
           },
@@ -280,6 +285,7 @@ export const indexCommand = new Command('index')
       let ghStats = { totalDocuments: 0, indexDuration: 0 };
       if (canIndexGitHub) {
         const ghStartTime = Date.now();
+        let ghEmbeddingStartTime = 0;
         const ghVectorPath = `${filePaths.vectors}-github`;
         const ghIndexer = new GitHubIndexer({
           vectorStorePath: ghVectorPath,
@@ -295,9 +301,14 @@ export const indexCommand = new Command('index')
             if (progress.phase === 'fetching') {
               progressRenderer.updateSection('Fetching issues/PRs...');
             } else if (progress.phase === 'embedding') {
-              const pct = Math.round((progress.documentsProcessed / progress.totalDocuments) * 100);
-              progressRenderer.updateSection(
-                `${progress.documentsProcessed}/${progress.totalDocuments} documents (${pct}%)`
+              if (ghEmbeddingStartTime === 0) {
+                ghEmbeddingStartTime = Date.now();
+              }
+              progressRenderer.updateSectionWithRate(
+                progress.documentsProcessed,
+                progress.totalDocuments,
+                'documents',
+                ghEmbeddingStartTime
               );
             }
           },
diff --git a/packages/cli/src/commands/update.ts b/packages/cli/src/commands/update.ts
index 6ac2c4f..d17e84a 100644
--- a/packages/cli/src/commands/update.ts
+++ b/packages/cli/src/commands/update.ts
@@ -83,12 +83,67 @@ export const updateCommand = new Command('update')
 
       await indexer.initialize();
 
-      // Create logger for updating (verbose mode shows debug logs)
-      const indexLogger = createIndexLogger(options.verbose);
+      // Get update plan to show user what will be updated
+      const updatePlan = await indexer.getUpdatePlan();
 
-      // Stop spinner and switch to section-based progress
+      // Stop spinner
       spinner.stop();
 
+      if (!updatePlan || updatePlan.total === 0) {
+        output.success('No changes detected');
+        await indexer.close();
+        metricsStore.close();
+        return;
+      }
+
+      // Show update plan
+      console.log('');
+      console.log(chalk.bold('Update plan:'));
+      console.log('');
+
+      if (updatePlan.added.length > 0) {
+        console.log(chalk.green(`  ✓ ${updatePlan.added.length} new file(s)`));
+        if (options.verbose) {
+          for (const file of updatePlan.added.slice(0, 5)) {
+            console.log(chalk.dim(`    + ${file}`));
+          }
+          if (updatePlan.added.length > 5) {
+            console.log(chalk.dim(`    ... and ${updatePlan.added.length - 5} more`));
+          }
+        }
+      }
+
+      if (updatePlan.changed.length > 0) {
+        console.log(chalk.yellow(`  ↻ ${updatePlan.changed.length} modified file(s)`));
+        if (options.verbose) {
+          for (const file of updatePlan.changed.slice(0, 5)) {
+            console.log(chalk.dim(`    ~ ${file}`));
+          }
+          if (updatePlan.changed.length > 5) {
+            console.log(chalk.dim(`    ... and ${updatePlan.changed.length - 5} more`));
+          }
+        }
+      }
+
+      if (updatePlan.deleted.length > 0) {
+        console.log(chalk.red(`  ✗ ${updatePlan.deleted.length} deleted file(s)`));
+        if (options.verbose) {
+          for (const file of updatePlan.deleted.slice(0, 5)) {
+            console.log(chalk.dim(`    - ${file}`));
+          }
+          if (updatePlan.deleted.length > 5) {
+            console.log(chalk.dim(`    ... and ${updatePlan.deleted.length - 5} more`));
+          }
+        }
+      }
+
+      console.log('');
+      console.log(chalk.dim(`Total: ${updatePlan.total} file(s) to process`));
+      console.log('');
+
+      // Create logger for updating (verbose mode shows debug logs)
+      const indexLogger = createIndexLogger(options.verbose);
+
       // Initialize progress renderer
       const progressRenderer = new ProgressRenderer({ verbose: options.verbose });
       progressRenderer.setSections(['Scanning Changed Files', 'Embedding Vectors']);
@@ -114,17 +169,20 @@ export const updateCommand = new Command('update')
             }
 
             // Update embedding progress
-            const pct = Math.round((progress.documentsIndexed / progress.totalDocuments) * 100);
-            const embeddingElapsed = (Date.now() - embeddingStartTime) / 1000;
-            const docsPerSec =
-              embeddingElapsed > 0 ? progress.documentsIndexed / embeddingElapsed : 0;
-            progressRenderer.updateSection(
-              `${progress.documentsIndexed.toLocaleString()}/${progress.totalDocuments.toLocaleString()} documents (${pct}%, ${docsPerSec.toFixed(0)} docs/sec)`
+            progressRenderer.updateSectionWithRate(
+              progress.documentsIndexed,
+              progress.totalDocuments,
+              'documents',
+              embeddingStartTime
             );
           } else {
             // Scanning phase
-            const percent = progress.percentComplete || 0;
-            progressRenderer.updateSection(`${percent.toFixed(0)}% complete`);
+            progressRenderer.updateSectionWithRate(
+              progress.filesProcessed,
+              progress.totalFiles,
+              'files',
+              scanStartTime
+            );
           }
         },
       });
@@ -155,13 +213,9 @@ export const updateCommand = new Command('update')
 
       // Show completion message
       output.log('');
-      if (stats.filesScanned === 0) {
-        output.success('No changes detected');
-      } else {
-        output.success(
-          `Updated ${stats.filesScanned.toLocaleString()} files in ${duration.toFixed(1)}s`
-        );
-      }
+      output.success(
+        `Updated ${stats.filesScanned.toLocaleString()} files in ${duration.toFixed(1)}s`
+      );
       output.log('');
 
       // Show errors if any
diff --git a/packages/cli/src/utils/progress.ts b/packages/cli/src/utils/progress.ts
index 78d9476..8947360 100644
--- a/packages/cli/src/utils/progress.ts
+++ b/packages/cli/src/utils/progress.ts
@@ -56,6 +56,23 @@ export class ProgressRenderer {
     }
   }
 
+  /**
+   * Update section with formatted progress including rate
+   */
+  updateSectionWithRate(processed: number, total: number, unit: string, startTime: number): void {
+    if (total === 0) {
+      this.updateSection('Discovering...');
+      return;
+    }
+
+    const pct = Math.round((processed / total) * 100);
+    const elapsed = (Date.now() - startTime) / 1000;
+    const rate = elapsed > 0 ? processed / elapsed : 0;
+    this.updateSection(
+      `${processed.toLocaleString()}/${total.toLocaleString()} ${unit} (${pct}%, ${rate.toFixed(0)} ${unit}/sec)`
+    );
+  }
+
   /**
    * Mark current section as complete and move to next
    */
diff --git a/packages/core/src/indexer/index.ts b/packages/core/src/indexer/index.ts
index ac08faf..e23270b 100644
--- a/packages/core/src/indexer/index.ts
+++ b/packages/core/src/indexer/index.ts
@@ -591,6 +591,29 @@ export class RepositoryIndexer {
     return validation.data;
   }
 
+  /**
+   * Get update plan showing which files will be processed
+   * Useful for displaying a plan before running update
+   */
+  async getUpdatePlan(options: { since?: Date } = {}): Promise<{
+    changed: string[];
+    added: string[];
+    deleted: string[];
+    total: number;
+  } | null> {
+    if (!this.state) {
+      return null;
+    }
+
+    const { changed, added, deleted } = await this.detectChangedFiles(options.since);
+    return {
+      changed,
+      added,
+      deleted,
+      total: changed.length + added.length + deleted.length,
+    };
+  }
+
   /**
    * Enrich language stats with change frequency data
    * Non-blocking: returns original stats if git analysis fails
diff --git a/packages/core/src/map/index.ts b/packages/core/src/map/index.ts
index a8957bf..802a3e7 100644
--- a/packages/core/src/map/index.ts
+++ b/packages/core/src/map/index.ts
@@ -486,6 +486,26 @@ function computeHotPaths(docs: SearchResult[], maxPaths: number): HotPath[] {
   return sorted;
 }
 
+/**
+ * Get file icon based on extension
+ */
+function getFileIcon(ext: string): string {
+  const iconMap: Record<string, string> = {
+    ts: '📘',
+    tsx: '⚛️',
+    js: '📜',
+    jsx: '⚛️',
+    go: '🐹',
+    py: '🐍',
+    rs: '🦀',
+    md: '📝',
+    json: '📋',
+    yaml: '⚙️',
+    yml: '⚙️',
+  };
+  return iconMap[ext] || '📄';
+}
+
 /**
  * Format codebase map as readable text
  */
@@ -501,8 +521,20 @@ export function formatCodebaseMap(map: CodebaseMap, options: MapOptions = {}): s
     lines.push('## Hot Paths (most referenced)');
     for (let i = 0; i < map.hotPaths.length; i++) {
       const hp = map.hotPaths[i];
-      const component = hp.primaryComponent ? ` (${hp.primaryComponent})` : '';
-      lines.push(`${i + 1}. \`${hp.file}\`${component} - ${hp.incomingRefs} refs`);
+      const isLast = i === map.hotPaths.length - 1;
+      const prefix = isLast ? '└─' : '├─';
+
+      // Get file extension for icon
+      const ext = hp.file.split('.').pop() || '';
+      const icon = getFileIcon(ext);
+
+      // Extract just the filename for cleaner display
+      const fileName = hp.file.split('/').pop() || hp.file;
+      const dirPath = hp.file.substring(0, hp.file.lastIndexOf('/'));
+
+      const component = hp.primaryComponent ? ` • ${hp.primaryComponent}` : '';
+      lines.push(`  ${prefix} ${icon} **${fileName}**${component} • ${hp.incomingRefs} refs`);
+      lines.push(`     ${dirPath}`);
     }
     lines.push('');
   }

From d24f2a8f8932ae37f133206d2ba925480193fe13 Mon Sep 17 00:00:00 2001
From: prosdev <prosdev@users.noreply.github.com>
Date: Sat, 13 Dec 2025 20:17:25 -0800
Subject: [PATCH 3/4] feat(cli): improve visual formatting and fix GitHub stats

Visual Improvements:
- Add tree branches and file icons to 'dev map' hot paths
- Add tree branches and file icons to 'dev activity' output
- Extract getFileIcon() to shared utility in @lytics/dev-agent-core

GitHub Stats Fix:
- Track issue and PR states separately (issuesByState, prsByState)
- Fix confusing display showing '14 open PRs' when there were 0
- Add proper per-type state counts to GitHubIndexStats interface
- Update display to show accurate counts for issues and PRs

Progress Display Enhancements:
- Add detailed scanning progress with rates (e.g., '1,234/4,567 files (27%, 45 files/sec)')
- Extend detailed progress to 'dev update', 'dev git index', and 'dev github index'
- Add update plan display to 'dev update' (shows changed/added/deleted before starting)
- Refactor progress formatting into reusable updateSectionWithRate() method
- Fix NaN display when totalFiles is 0 (now shows 'Discovering files...')

Test Updates:
- Update map test to match new hot paths format with tree branches

All visual outputs now use consistent tree-based formatting with file icons.
---
 packages/cli/src/commands/activity.ts       | 50 ++++++++++-----------
 packages/cli/src/commands/stats.ts          |  4 ++
 packages/cli/src/utils/output.ts            | 50 +++++++++++++--------
 packages/core/src/map/__tests__/map.test.ts |  3 +-
 packages/core/src/map/index.ts              | 21 +--------
 packages/core/src/utils/icons.ts            | 27 +++++++++++
 packages/core/src/utils/index.ts            |  1 +
 packages/subagents/src/github/indexer.ts    | 21 +++++++++
 packages/types/src/github.ts                |  8 +++-
 9 files changed, 117 insertions(+), 68 deletions(-)
 create mode 100644 packages/core/src/utils/icons.ts

diff --git a/packages/cli/src/commands/activity.ts b/packages/cli/src/commands/activity.ts
index 2c6fb54..58c9c63 100644
--- a/packages/cli/src/commands/activity.ts
+++ b/packages/cli/src/commands/activity.ts
@@ -5,6 +5,7 @@
 import * as path from 'node:path';
 import {
   type FileMetrics,
+  getFileIcon,
   getMostActive,
   getStoragePath,
   MetricsStore,
@@ -31,43 +32,38 @@ function formatRelativeTime(date: Date): string {
 }
 
 /**
- * Format files as a compact table
+ * Format files with tree branches and icons
  */
 function formatFileMetricsTable(files: FileMetrics[]): string {
   if (files.length === 0) return '';
 
-  // Calculate column widths
-  const maxPathLen = Math.max(...files.map((f) => f.filePath.length), 40);
-  const pathWidth = Math.min(maxPathLen, 55);
+  let output = '';
 
-  // Header
-  let output = chalk.bold(
-    `${'FILE'.padEnd(pathWidth)}  ${'COMMITS'.padStart(7)}  ${'LOC'.padStart(6)}  ${'AUTHORS'.padStart(7)}  ${'LAST CHANGE'}\n`
-  );
+  for (let i = 0; i < files.length; i++) {
+    const file = files[i];
+    const isLast = i === files.length - 1;
+    const branch = isLast ? '└─' : '├─';
+    const connector = isLast ? ' ' : '│'; // Vertical line for non-last items
+    const icon = getFileIcon(file.filePath);
 
-  // Separator line
-  output += chalk.dim(`${'─'.repeat(pathWidth + 2 + 7 + 2 + 6 + 2 + 7 + 2 + 12)}\n`);
-
-  // Rows
-  for (const file of files) {
-    // Truncate path if too long
-    let displayPath = file.filePath;
-    if (displayPath.length > pathWidth) {
-      displayPath = `...${displayPath.slice(-(pathWidth - 3))}`;
-    }
-    displayPath = displayPath.padEnd(pathWidth);
-
-    const commits = String(file.commitCount).padStart(7);
-    const loc = String(file.linesOfCode).padStart(6);
-
-    // Author count with emoji
-    const authorIcon = file.authorCount === 1 ? ' 👤' : file.authorCount === 2 ? ' 👥' : '👥👥';
-    const authors = `${String(file.authorCount).padStart(5)}${authorIcon}`;
+    // Author info
+    const authorIcon = file.authorCount === 1 ? '👤' : file.authorCount === 2 ? '👥' : '👥👥';
 
     // Relative time
     const lastChange = file.lastModified ? formatRelativeTime(file.lastModified) : 'unknown';
 
-    output += `${chalk.dim(displayPath)}  ${chalk.cyan(commits)}  ${chalk.yellow(loc)}  ${chalk.green(authors)}  ${chalk.gray(lastChange)}\n`;
+    // File path line with icon and branch
+    output += `${chalk.dim(branch)} ${icon} ${file.filePath}\n`;
+
+    // Metrics line with vertical connector
+    output += chalk.dim(
+      `${connector}     ${file.commitCount} commits • ${file.authorCount} ${authorIcon} • Last: ${lastChange}\n`
+    );
+
+    // Add vertical line separator between items (except after last)
+    if (!isLast) {
+      output += chalk.dim(`${connector}\n`);
+    }
   }
 
   return output;
diff --git a/packages/cli/src/commands/stats.ts b/packages/cli/src/commands/stats.ts
index bed5dd2..c3bb173 100644
--- a/packages/cli/src/commands/stats.ts
+++ b/packages/cli/src/commands/stats.ts
@@ -100,6 +100,8 @@ async function loadCurrentStats(): Promise<{
       totalDocuments: state.totalDocuments || 0,
       byType: state.byType || {},
       byState: state.byState || {},
+      issuesByState: state.issuesByState,
+      prsByState: state.prsByState,
       lastIndexed: state.lastIndexed || '',
       indexDuration: state.indexDuration || 0,
     };
@@ -217,6 +219,8 @@ What You'll See:
               totalDocuments: number;
               byType: { issue?: number; pull_request?: number };
               byState: { open?: number; closed?: number; merged?: number };
+              issuesByState?: { open: number; closed: number };
+              prsByState?: { open: number; closed: number; merged: number };
               lastIndexed: string;
             } | null) || undefined,
         });
diff --git a/packages/cli/src/utils/output.ts b/packages/cli/src/utils/output.ts
index f67b95d..100b4cb 100644
--- a/packages/cli/src/utils/output.ts
+++ b/packages/cli/src/utils/output.ts
@@ -142,18 +142,26 @@ export function formatGitHubSummary(githubStats: {
   totalDocuments: number;
   byType: { issue?: number; pull_request?: number };
   byState: { open?: number; closed?: number; merged?: number };
+  issuesByState?: { open: number; closed: number };
+  prsByState?: { open: number; closed: number; merged: number };
   lastIndexed: string;
 }): string {
   const issues = githubStats.byType.issue || 0;
   const prs = githubStats.byType.pull_request || 0;
-  const open = githubStats.byState.open || 0;
-  const merged = githubStats.byState.merged || 0;
+
+  // Use per-type state counts if available (new format), fall back to aggregate (old format)
+  const issuesOpen = githubStats.issuesByState?.open ?? 0;
+  const issuesClosed = githubStats.issuesByState?.closed ?? 0;
+  const prsOpen = githubStats.prsByState?.open ?? 0;
+  const prsMerged = githubStats.prsByState?.merged ?? 0;
 
   const timeSince = getTimeSince(new Date(githubStats.lastIndexed));
 
   return [
     `🔗 ${chalk.bold(githubStats.repository)} • ${formatNumber(githubStats.totalDocuments)} documents`,
-    `   ${chalk.gray(issues.toString())} issues • ${chalk.gray(prs.toString())} PRs • ${chalk.gray(open.toString())} open • ${chalk.gray(merged.toString())} merged • Synced ${timeSince}`,
+    `   Issues: ${chalk.gray(issues.toString())} total (${issuesOpen} open, ${issuesClosed} closed)`,
+    `   Pull Requests: ${chalk.gray(prs.toString())} total (${prsOpen} open, ${prsMerged} merged)`,
+    `   Last synced: ${timeSince}`,
   ].join('\n');
 }
 
@@ -369,6 +377,8 @@ export function printRepositoryStats(data: {
     totalDocuments: number;
     byType: { issue?: number; pull_request?: number };
     byState: { open?: number; closed?: number; merged?: number };
+    issuesByState?: { open: number; closed: number };
+    prsByState?: { open: number; closed: number; merged: number };
     lastIndexed: string;
   } | null;
 }): void {
@@ -471,19 +481,21 @@ export function printRepositoryStats(data: {
     const issues = githubStats.byType.issue || 0;
     const prs = githubStats.byType.pull_request || 0;
 
+    // Use per-type state counts if available (new format), fall back to aggregate (old format)
+    const issuesOpen = githubStats.issuesByState?.open ?? githubStats.byState.open ?? 0;
+    const issuesClosed = githubStats.issuesByState?.closed ?? githubStats.byState.closed ?? 0;
+    const prsOpen = githubStats.prsByState?.open ?? githubStats.byState.open ?? 0;
+    const prsMerged = githubStats.prsByState?.merged ?? githubStats.byState.merged ?? 0;
+
     if (issues > 0) {
-      const openIssues = githubStats.byState.open || 0;
-      const closedIssues = githubStats.byState.closed || 0;
       output.log(
-        `  Issues: ${chalk.bold(issues.toString())} total (${chalk.green(`${openIssues} open`)}, ${chalk.gray(`${closedIssues} closed`)})`
+        `  Issues: ${chalk.bold(issues.toString())} total (${issuesOpen} open, ${issuesClosed} closed)`
       );
     }
 
     if (prs > 0) {
-      const openPRs = githubStats.byState.open || 0;
-      const mergedPRs = githubStats.byState.merged || 0;
       output.log(
-        `  Pull Requests: ${chalk.bold(prs.toString())} total (${chalk.green(`${openPRs} open`)}, ${chalk.magenta(`${mergedPRs} merged`)})`
+        `  Pull Requests: ${chalk.bold(prs.toString())} total (${prsOpen} open, ${prsMerged} merged)`
       );
     }
 
@@ -905,6 +917,8 @@ export function printGitHubStats(githubStats: {
   totalDocuments: number;
   byType: { issue?: number; pull_request?: number; discussion?: number };
   byState: { open?: number; closed?: number; merged?: number };
+  issuesByState?: { open: number; closed: number };
+  prsByState?: { open: number; closed: number; merged: number };
   lastIndexed: string;
   indexDuration?: number;
 }): void {
@@ -912,9 +926,12 @@ export function printGitHubStats(githubStats: {
   const prs = githubStats.byType.pull_request || 0;
   const discussions = githubStats.byType.discussion || 0;
 
-  const openCount = githubStats.byState.open || 0;
-  const closedCount = githubStats.byState.closed || 0;
-  const mergedCount = githubStats.byState.merged || 0;
+  // Use per-type state counts if available (new format), fall back to aggregate (old format)
+  const issueOpen = githubStats.issuesByState?.open ?? 0;
+  const issueClosed = githubStats.issuesByState?.closed ?? 0;
+  const prOpen = githubStats.prsByState?.open ?? 0;
+  const prClosed = githubStats.prsByState?.closed ?? 0;
+  const prMerged = githubStats.prsByState?.merged ?? 0;
 
   const timeSince = getTimeSince(new Date(githubStats.lastIndexed));
 
@@ -928,9 +945,6 @@ export function printGitHubStats(githubStats: {
   // Issues breakdown
   if (issues > 0) {
     const issueStates: string[] = [];
-    // Calculate issue-specific counts (open + closed, no merged for issues)
-    const issueOpen = openCount > 0 ? openCount : 0;
-    const issueClosed = closedCount > 0 ? closedCount : 0;
 
     if (issueOpen > 0) {
       issueStates.push(`${chalk.green('●')} ${issueOpen} open`);
@@ -949,13 +963,13 @@ export function printGitHubStats(githubStats: {
   // Pull requests breakdown
   if (prs > 0) {
     const prStates: string[] = [];
-    // For PRs, we show open and merged
-    const prOpen = openCount > 0 ? openCount : 0;
-    const prMerged = mergedCount > 0 ? mergedCount : 0;
 
     if (prOpen > 0) {
       prStates.push(`${chalk.green('●')} ${prOpen} open`);
     }
+    if (prClosed > 0) {
+      prStates.push(`${chalk.gray('●')} ${prClosed} closed`);
+    }
     if (prMerged > 0) {
       prStates.push(`${chalk.magenta('●')} ${prMerged} merged`);
     }
diff --git a/packages/core/src/map/__tests__/map.test.ts b/packages/core/src/map/__tests__/map.test.ts
index 7d28e4d..76aa911 100644
--- a/packages/core/src/map/__tests__/map.test.ts
+++ b/packages/core/src/map/__tests__/map.test.ts
@@ -485,8 +485,9 @@ describe('Codebase Map', () => {
       const output = formatCodebaseMap(map, { includeHotPaths: true });
 
       expect(output).toContain('## Hot Paths');
-      expect(output).toContain('src/core.ts');
+      expect(output).toContain('**core.ts**'); // Filename in bold
       expect(output).toContain('2 refs');
+      expect(output).toContain('src'); // Directory path on separate line
     });
   });
 
diff --git a/packages/core/src/map/index.ts b/packages/core/src/map/index.ts
index 802a3e7..e8f96c2 100644
--- a/packages/core/src/map/index.ts
+++ b/packages/core/src/map/index.ts
@@ -7,6 +7,7 @@ import * as path from 'node:path';
 import type { Logger } from '@lytics/kero';
 import type { LocalGitExtractor } from '../git/extractor';
 import type { RepositoryIndexer } from '../indexer';
+import { getFileIcon } from '../utils/icons';
 import type { SearchResult } from '../vector/types';
 import type {
   ChangeFrequency,
@@ -486,26 +487,6 @@ function computeHotPaths(docs: SearchResult[], maxPaths: number): HotPath[] {
   return sorted;
 }
 
-/**
- * Get file icon based on extension
- */
-function getFileIcon(ext: string): string {
-  const iconMap: Record<string, string> = {
-    ts: '📘',
-    tsx: '⚛️',
-    js: '📜',
-    jsx: '⚛️',
-    go: '🐹',
-    py: '🐍',
-    rs: '🦀',
-    md: '📝',
-    json: '📋',
-    yaml: '⚙️',
-    yml: '⚙️',
-  };
-  return iconMap[ext] || '📄';
-}
-
 /**
  * Format codebase map as readable text
  */
diff --git a/packages/core/src/utils/icons.ts b/packages/core/src/utils/icons.ts
new file mode 100644
index 0000000..a40b865
--- /dev/null
+++ b/packages/core/src/utils/icons.ts
@@ -0,0 +1,27 @@
+/**
+ * Utility functions for file and UI icons
+ */
+
+/**
+ * Get file icon based on extension
+ */
+export function getFileIcon(filePathOrExt: string): string {
+  // Extract extension (handle both full paths and just extensions)
+  const ext = filePathOrExt.includes('.') ? filePathOrExt.split('.').pop() || '' : filePathOrExt;
+
+  const iconMap: Record<string, string> = {
+    ts: '📘',
+    tsx: '⚛️',
+    js: '📜',
+    jsx: '⚛️',
+    go: '🐹',
+    py: '🐍',
+    rs: '🦀',
+    md: '📝',
+    json: '📋',
+    yaml: '⚙️',
+    yml: '⚙️',
+  };
+
+  return iconMap[ext] || '📄';
+}
diff --git a/packages/core/src/utils/index.ts b/packages/core/src/utils/index.ts
index 0a7212b..f503524 100644
--- a/packages/core/src/utils/index.ts
+++ b/packages/core/src/utils/index.ts
@@ -4,5 +4,6 @@
 
 export * from './concurrency';
 export * from './file-validator';
+export * from './icons';
 export * from './retry';
 export * from './wasm-resolver';
diff --git a/packages/subagents/src/github/indexer.ts b/packages/subagents/src/github/indexer.ts
index 10914d3..408fd51 100644
--- a/packages/subagents/src/github/indexer.ts
+++ b/packages/subagents/src/github/indexer.ts
@@ -178,6 +178,21 @@ export class GitHubIndexer {
       {} as Record<string, number>
     );
 
+    // Calculate states per type for accurate reporting
+    const issuesByState = { open: 0, closed: 0 };
+    const prsByState = { open: 0, closed: 0, merged: 0 };
+
+    for (const doc of enrichedDocs) {
+      if (doc.type === 'issue') {
+        if (doc.state === 'open') issuesByState.open++;
+        else if (doc.state === 'closed') issuesByState.closed++;
+      } else if (doc.type === 'pull_request') {
+        if (doc.state === 'open') prsByState.open++;
+        else if (doc.state === 'closed') prsByState.closed++;
+        else if (doc.state === 'merged') prsByState.merged++;
+      }
+    }
+
     // Update state
     this.state = {
       version: INDEXER_VERSION,
@@ -186,6 +201,8 @@ export class GitHubIndexer {
       totalDocuments: enrichedDocs.length,
       byType: byType as Record<'issue' | 'pull_request' | 'discussion', number>,
       byState: byState as Record<'open' | 'closed' | 'merged', number>,
+      issuesByState,
+      prsByState,
     };
 
     // Save state to disk
@@ -202,6 +219,8 @@ export class GitHubIndexer {
       totalDocuments: enrichedDocs.length,
       byType: byType as Record<'issue' | 'pull_request' | 'discussion', number>,
       byState: byState as Record<'open' | 'closed' | 'merged', number>,
+      issuesByState,
+      prsByState,
       lastIndexed: this.state.lastIndexed,
       indexDuration: durationMs,
     };
@@ -398,6 +417,8 @@ export class GitHubIndexer {
       totalDocuments: this.state.totalDocuments,
       byType: this.state.byType,
       byState: this.state.byState,
+      issuesByState: this.state.issuesByState,
+      prsByState: this.state.prsByState,
       lastIndexed: this.state.lastIndexed,
       indexDuration: 0,
     };
diff --git a/packages/types/src/github.ts b/packages/types/src/github.ts
index 948b0c3..b406576 100644
--- a/packages/types/src/github.ts
+++ b/packages/types/src/github.ts
@@ -110,7 +110,9 @@ export interface GitHubIndexerState {
   lastIndexed: string; // ISO date
   totalDocuments: number;
   byType: Record<GitHubDocumentType, number>;
-  byState: Record<GitHubState, number>;
+  byState: Record<GitHubState, number>; // Deprecated: aggregate counts (kept for compatibility)
+  issuesByState: { open: number; closed: number };
+  prsByState: { open: number; closed: number; merged: number };
 }
 
 /**
@@ -145,7 +147,9 @@ export interface GitHubIndexStats {
   repository: string;
   totalDocuments: number;
   byType: Record<GitHubDocumentType, number>;
-  byState: Record<GitHubState, number>;
+  byState: Record<GitHubState, number>; // Deprecated: aggregate counts (kept for compatibility)
+  issuesByState: { open: number; closed: number };
+  prsByState: { open: number; closed: number; merged: number };
   lastIndexed: string; // ISO date
   indexDuration: number; // milliseconds
 }

From 05e89a1a509af704da668e602e0f09f682320189 Mon Sep 17 00:00:00 2001
From: prosdev <prosdev@users.noreply.github.com>
Date: Sat, 13 Dec 2025 20:19:49 -0800
Subject: [PATCH 4/4] chore: add changeset for visual formatting and GitHub
 stats improvements

---
 .../visual-formatting-and-github-stats-fix.md | 99 +++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 .changeset/visual-formatting-and-github-stats-fix.md

diff --git a/.changeset/visual-formatting-and-github-stats-fix.md b/.changeset/visual-formatting-and-github-stats-fix.md
new file mode 100644
index 0000000..122b26b
--- /dev/null
+++ b/.changeset/visual-formatting-and-github-stats-fix.md
@@ -0,0 +1,99 @@
+---
+"@lytics/dev-agent-cli": patch
+"@lytics/dev-agent-core": patch
+"@lytics/dev-agent-subagents": patch
+"@lytics/dev-agent-types": patch
+"dev-agent": patch
+---
+
+# Visual Formatting & GitHub Stats Improvements
+
+## Visual Enhancements ✨
+
+### Tree Branches & File Icons
+All CLI outputs now use consistent tree-based formatting with file icons:
+
+**`dev map` hot paths:**
+```
+## Hot Paths (most referenced)
+  ├─ 📘 **typescript.ts** • 307 refs
+     /packages/core/src/scanner
+  ├─ 📘 **index.ts** • 251 refs
+     /packages/core/src/indexer
+  └─ 📘 **go.ts** • 152 refs
+     /packages/core/src/scanner
+```
+
+**`dev activity` output:**
+```
+├─ 📘 packages/mcp-server/bin/dev-agent-mcp.ts
+│     34 commits • 1 👤 • Last: today
+│
+├─ 📘 packages/core/src/indexer/index.ts
+│     32 commits • 1 👤 • Last: today
+```
+
+### Shared Icon Utility
+Extracted `getFileIcon()` to `@lytics/dev-agent-core/utils` for reuse across packages.
+
+## GitHub Stats Fix 🐛
+
+Fixed confusing issue/PR state display:
+
+**Before:**
+```
+Issues: 68 total (14 open, 55 closed)
+Pull Requests: 97 total (14 open, 96 merged)  ❌ Wrong!
+```
+
+**After:**
+```
+Issues: 68 total (14 open, 54 closed)
+Pull Requests: 97 total (0 open, 96 merged)   ✅ Correct!
+```
+
+- Added separate state tracking: `issuesByState`, `prsByState`
+- GitHub indexer now tracks issue and PR states independently
+- Stats display now shows accurate per-type counts
+
+## Progress Display Improvements 📊
+
+### Detailed Progress with Rates
+All indexing commands now show detailed progress:
+
+```
+Scanning Repository: 1,234/4,567 files (27%, 45 files/sec)
+Embedding Vectors: 856/2,549 documents (34%, 122 docs/sec)
+```
+
+Applied to:
+- `dev index` - scanning & embedding progress
+- `dev update` - changed files & embedding progress
+- `dev git index` - commit embedding progress
+- `dev github index` - document embedding progress
+
+### Update Plan Display
+`dev update` now shows what will change before starting:
+
+```
+Update plan:
+  • Changed: 3 files
+  • Added: 1 file
+  • Deleted: 0 files
+```
+
+### Code Quality
+- Refactored progress logic into `ProgressRenderer.updateSectionWithRate()`
+- Reduced ~40 lines of duplicated code
+- Fixed NaN display (now shows "Discovering files..." initially)
+
+## Bug Fixes 🐛
+
+- **`dev owners`**: Fixed "No ownership data" error when run from subdirectories
+- **Progress Display**: Fixed NaN showing during initial file discovery phase
+- **`dev update`**: Removed duplicate checkmark in success message
+
+## Breaking Changes
+
+None - all changes are backward compatible. Old GitHub state files will fall back to aggregate counts gracefully.
+