Updated to work a lot better.

app.py

@@ -8,11 +8,12 @@ import subprocess
 import json
 from pathlib import Path
 from datetime import datetime
-from flask import Flask, render_template, request, jsonify
+from flask import Flask, render_template, request, jsonify, send_file
 from apscheduler.schedulers.background import BackgroundScheduler
 from apscheduler.triggers.cron import CronTrigger
 import markdown
 import logging
+import re
 from whoosh.index import create_in, open_dir
 from whoosh.fields import Schema, TEXT, ID
 from whoosh.qparser import QueryParser
@@ -48,6 +49,88 @@ def create_search_index():
 
 ix = create_search_index()
 
+def is_hidden_path(file_path):
+    """Check if a file path contains any hidden directories or files (starting with dot)."""
+    path_obj = Path(file_path) if isinstance(file_path, str) else file_path
+    # Check all parts of the path including the filename
+    return any(part.startswith('.') for part in path_obj.parts)
+
+def rewrite_image_paths(md_content, repo, filepath):
+    """Rewrite relative image paths to be served by Flask."""
+    # Get the directory of the current file (relative to repo root)
+    file_dir = os.path.dirname(filepath)
+    
+    # Pattern to match markdown image syntax: ![alt](path)
+    def replace_image_path(match):
+        alt_text = match.group(1)
+        img_path = match.group(2)
+        
+        # Skip absolute URLs and data URIs
+        if img_path.startswith(('http://', 'https://', 'data:')):
+            return match.group(0)
+        
+        # Resolve relative paths
+        if img_path.startswith('/'):
+            # Absolute path from repo root
+            resolved_path = img_path.lstrip('/')
+        else:
+            # Relative path - resolve it relative to the file's directory
+            if file_dir:
+                resolved_path = os.path.normpath(os.path.join(file_dir, img_path))
+            else:
+                resolved_path = img_path
+        
+        # Ensure forward slashes for URL
+        resolved_path = resolved_path.replace(os.sep, '/')
+        image_url = f"/image/{repo}/{resolved_path}"
+        
+        return f"![{alt_text}]({image_url})"
+    
+    # Replace all markdown image references
+    md_content = re.sub(r'!\[([^\]]*)\]\(([^\)]+)\)', replace_image_path, md_content)
+    return md_content
+
+def build_directory_tree(repo_path):
+    """Build a hierarchical tree of markdown files organized by directory."""
+    tree = {}
+    
+    if not os.path.exists(repo_path):
+        logger.warning(f"Repo path does not exist: {repo_path}")
+        return tree
+    
+    file_count = 0
+    for md_file in Path(repo_path).rglob('*'):
+        if md_file.suffix.lower() not in MARKDOWN_EXTENSIONS:
+            continue
+        if is_hidden_path(md_file):
+            logger.debug(f"Skipping hidden path: {md_file}")
+            continue
+        
+        file_count += 1
+        rel_path = md_file.relative_to(repo_path)
+        parts = rel_path.parts[:-1]  # All parts except filename
+        filename = md_file.stem  # Name without extension
+        
+        logger.debug(f"Adding to tree: {rel_path} (name: {filename})")
+        
+        # Navigate/create nested dict structure
+        current = tree
+        for part in parts:
+            if part not in current:
+                current[part] = {}
+            current = current[part]
+        
+        # Add file to current level
+        if '_files' not in current:
+            current['_files'] = []
+        current['_files'].append({
+            'name': filename,
+            'path': str(rel_path)
+        })
+    
+    logger.info(f"Built tree for {repo_path}: found {file_count} markdown files")
+    return tree
+
 def load_repositories():
     """Load repository configuration from file."""
     if not os.path.exists(CONFIG_FILE):
@@ -115,7 +198,7 @@ def update_search_index():
                 continue
             
             for md_file in repo_dir.rglob('*'):
-                if md_file.suffix.lower() in MARKDOWN_EXTENSIONS:
+                if md_file.suffix.lower() in MARKDOWN_EXTENSIONS and not is_hidden_path(md_file):
                     try:
                         content = md_file.read_text(encoding='utf-8', errors='ignore')
                         # Extract title from filename or first heading
@@ -181,24 +264,43 @@ def index():
     
     for repo_name in repos.keys():
         repo_path = os.path.join(REPOS_DIR, repo_name)
-        markdown_files = []
-        
-        if os.path.exists(repo_path):
-            for md_file in Path(repo_path).rglob('*'):
-                if md_file.suffix.lower() in MARKDOWN_EXTENSIONS:
-                    rel_path = str(md_file.relative_to(repo_path))
-                    markdown_files.append({
-                        'name': md_file.stem,
-                        'path': rel_path
-                    })
+        file_tree = build_directory_tree(repo_path)
         
         repo_list.append({
             'name': repo_name,
-            'files': sorted(markdown_files, key=lambda x: x['path'])
+            'tree': file_tree
         })
     
     return render_template('index.html', repositories=repo_list)
 
+@app.route('/image/<repo>/<path:filepath>')
+def serve_image(repo, filepath):
+    """Serve images from repository directories."""
+    # Security: prevent directory traversal
+    if '..' in filepath or filepath.startswith('/'):
+        return "Invalid path", 400
+    
+    file_path = os.path.join(REPOS_DIR, repo, filepath)
+    
+    # Ensure the file is within the repo directory
+    try:
+        file_path = os.path.realpath(file_path)
+        repo_path = os.path.realpath(os.path.join(REPOS_DIR, repo))
+        if not file_path.startswith(repo_path):
+            return "Access denied", 403
+    except Exception:
+        return "Invalid path", 400
+    
+    if not os.path.exists(file_path):
+        logger.warning(f"Image not found: {file_path}")
+        return "Image not found", 404
+    
+    try:
+        return send_file(file_path)
+    except Exception as e:
+        logger.error(f"Error serving image {file_path}: {e}")
+        return f"Error serving image: {e}", 500
+
 @app.route('/api/search', methods=['GET'])
 def search():
     """Search markdown files."""
@@ -249,6 +351,9 @@ def view_file(repo, filepath):
         with open(file_path, 'r', encoding='utf-8') as f:
             md_content = f.read()
         
+        # Rewrite image paths to be served by Flask
+        md_content = rewrite_image_paths(md_content, repo, filepath)
+        
         # Convert markdown to HTML
         html_content = markdown.markdown(
             md_content,