From 8d030758bfb7d3bb457f274ac27c57d97741f494 Mon Sep 17 00:00:00 2001
From: Paul Payne <paul@payne.io>
Date: Thu, 30 Oct 2025 13:23:50 -0700
Subject: [PATCH 1/2] feat(collections): Enhance collection installation by
 linking resource directories for discovery

---
 amplifier_app_cli/collections/installer.py    | 15 ++++++++++++
 .../module_resolution/sources.py              | 23 +++++++++++--------
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/amplifier_app_cli/collections/installer.py b/amplifier_app_cli/collections/installer.py
index 1ab435e6..1f94cd16 100644
--- a/amplifier_app_cli/collections/installer.py
+++ b/amplifier_app_cli/collections/installer.py
@@ -232,6 +232,21 @@ def install_collection(
                         logger.debug(f"Copied pyproject.toml from {item.name}/ to collection root")
                         break
 
+        # Link resource directories from package to collection root for discovery
+        # (profiles, context, agents, scenario-tools, modules may be inside package after wheel extraction)
+        for resource_dir in ["profiles", "context", "agents", "scenario-tools", "modules"]:
+            root_resource = collection_path / resource_dir
+            if not root_resource.exists():
+                # Search for resource dir in package directories
+                for item in collection_path.iterdir():
+                    if item.is_dir() and not item.name.endswith(".dist-info") and not item.name.startswith("."):
+                        pkg_resource = item / resource_dir
+                        if pkg_resource.exists() and pkg_resource.is_dir():
+                            # Create symlink to avoid duplicating files
+                            root_resource.symlink_to(pkg_resource, target_is_directory=True)
+                            logger.debug(f"Linked {resource_dir}/ from {item.name}/ to collection root")
+                            break
+
         # Step 4: Install scenario tools (if any)
         installed_tools = install_scenario_tools(collection_path)
         if installed_tools:
diff --git a/amplifier_app_cli/module_resolution/sources.py b/amplifier_app_cli/module_resolution/sources.py
index 93405096..9b2a2d40 100644
--- a/amplifier_app_cli/module_resolution/sources.py
+++ b/amplifier_app_cli/module_resolution/sources.py
@@ -118,29 +118,34 @@ def resolve(self) -> Path:
         Raises:
             ModuleNotFoundError: Git clone failed
         """
-        # Generate cache key
-        cache_key = hashlib.sha256(f"{self.url}@{self.ref}".encode()).hexdigest()[:12]
+        # Generate cache key - include subdirectory to avoid collisions
+        # (same repo+ref with different subdirectories need separate caches)
+        cache_key_input = f"{self.url}@{self.ref}"
+        if self.subdirectory:
+            cache_key_input += f"#{self.subdirectory}"
+        cache_key = hashlib.sha256(cache_key_input.encode()).hexdigest()[:12]
         cache_path = self.cache_dir / cache_key / self.ref
 
-        # Add subdirectory if specified
-        final_path = cache_path / self.subdirectory if self.subdirectory else cache_path
-
         # Check cache
         if cache_path.exists() and self._is_valid_cache(cache_path):
             logger.debug(f"Using cached git module: {cache_path}")
-            return final_path
+            return cache_path
 
         # Download
+        # Note: uv installs the package content FROM subdirectory TO cache_path directly
+        # It does NOT create the subdirectory structure in the target
         logger.info(f"Downloading git module: {self.url}@{self.ref}")
         try:
             self._download_via_uv(cache_path)
         except subprocess.CalledProcessError as e:
             raise ModuleNotFoundError(f"Failed to download {self.url}@{self.ref}: {e}")
 
-        if not final_path.exists():
-            raise ModuleNotFoundError(f"Subdirectory not found after download: {self.subdirectory}")
+        # Verify installation worked
+        if not self._is_valid_cache(cache_path):
+            sub_info = f"#subdirectory={self.subdirectory}" if self.subdirectory else ""
+            raise ModuleNotFoundError(f"Failed to install module from {self.url}@{self.ref}{sub_info}")
 
-        return final_path
+        return cache_path
 
     def _is_valid_cache(self, cache_path: Path) -> bool:
         """Check if cache directory contains valid module."""

From 1784a1c73ec119fb50b1df863c50cd071b3c0183 Mon Sep 17 00:00:00 2001
From: Paul Payne <paul@payne.io>
Date: Thu, 30 Oct 2025 13:24:04 -0700
Subject: [PATCH 2/2] feat(profiles): Add profile markdown body to context for
 enhanced processing

---
 amplifier_app_cli/main.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/amplifier_app_cli/main.py b/amplifier_app_cli/main.py
index 08e796c0..e153aee1 100644
--- a/amplifier_app_cli/main.py
+++ b/amplifier_app_cli/main.py
@@ -1301,6 +1301,17 @@ async def _process_profile_mentions(session: AmplifierSession, profile_name: str
 
         logger.debug(f"Profile markdown body length: {len(markdown_body)} chars")
 
+        # First, add the profile's own markdown body as context
+        logger.info("Adding profile markdown body as context")
+        context = session.coordinator.get("context")
+        if context and hasattr(context, "add_message"):
+            profile_context_msg = {"role": "system", "content": markdown_body}
+            await context.add_message(profile_context_msg)
+            logger.info(f"Added profile markdown body ({len(markdown_body)} chars) to context")
+        else:
+            logger.warning("Context not available, cannot add profile markdown body")
+
+        # Then, check for @mentions and load referenced files
         if not has_mentions(markdown_body):
             logger.debug("No @mentions found in profile markdown")
             return