Refactor cache access to use cache_manager consistently

- Remove symlink hack from cache_file() - no longer needed
- Add get_cache_path() helper for content_hash lookups
- Update all CACHE_DIR / content_hash patterns to use cache_manager
- Fix cache_manager.get_by_content_hash() to check path.exists()
- Fix legacy path lookup (cache_dir not legacy_dir)
- Update upload endpoint to use cache_manager.put()

This ensures cache lookups work correctly for both legacy files
(stored directly in CACHE_DIR) and new files (stored in nodes/).

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cache_manager.py

@@ -243,25 +243,25 @@ class L1CacheManager:
 
     def get_by_content_hash(self, content_hash: str) -> Optional[Path]:
         """Get cached file path by content_hash."""
-        # Check index first
+        # Check index first (new cache structure)
         node_id = self._content_index.get(content_hash)
         if node_id:
             path = self.cache.get(node_id)
-            if path:
+            if path and path.exists():
                 return path
 
-        # Check legacy directory
-        legacy_path = self.legacy_dir / content_hash
-        if legacy_path.exists():
-            return legacy_path
-
-        # Scan cache entries (fallback)
+        # Scan cache entries (fallback for new structure)
         entry = self.cache.find_by_content_hash(content_hash)
-        if entry:
+        if entry and entry.output_path.exists():
             self._content_index[content_hash] = entry.node_id
             self._save_content_index()
             return entry.output_path
 
+        # Check legacy location (files stored directly as CACHE_DIR/{content_hash})
+        legacy_path = self.cache_dir / content_hash
+        if legacy_path.exists() and legacy_path.is_file():
+            return legacy_path
+
         return None
 
     def has_content(self, content_hash: str) -> bool: