diff --git a/apps/api/src/api/tool_instances.py b/apps/api/src/api/tool_instances.py
index 02a3c07..d1cd5a8 100644
--- a/apps/api/src/api/tool_instances.py
+++ b/apps/api/src/api/tool_instances.py
@@ -143,11 +143,14 @@ async def _resolve_single_git_mount(
     
     # Handle branch checkout if specified
     if branch and repo_path:
-        try:
-            await asyncio.to_thread(_checkout_branch, repo_path, branch)
+        success = await asyncio.to_thread(_checkout_branch, repo_path, branch)
+        if success:
             logger.info("Checked out branch %s for %s", branch, remote_url)
-        except Exception as exc:
-            logger.warning("Branch checkout failed for %s@%s: %s", remote_url, branch, exc)
+        else:
+            logger.warning(
+                "Branch %s not found in %s, using current branch",
+                branch, remote_url
+            )
     
     # Build source path and expand globs
     if source_path and source_path != ".":
@@ -186,8 +189,12 @@ async def _resolve_single_git_mount(
     return volume_mounts
 
 
-def _checkout_branch(repo_path: str, branch: str) -> None:
-    """Checkout a specific branch in a git repository."""
+def _checkout_branch(repo_path: str, branch: str) -> bool:
+    """Checkout a specific branch in a git repository.
+    
+    Returns True if checkout succeeded, False if it failed.
+    On failure, the repository remains on its current branch.
+    """
     import subprocess
     
     # First try to checkout existing branch
@@ -211,7 +218,10 @@ def _checkout_branch(repo_path: str, branch: str) -> None:
         )
         
         if result.returncode != 0:
-            raise RuntimeError(f"Failed to checkout branch {branch}: {result.stderr}")
+            logger.warning("Failed to checkout branch %s in %s: %s", branch, repo_path, result.stderr.strip())
+            return False
+    
+    return True
 
 
 def _pull_repository_updates(repo_path: str, remote_url: str) -> None:
@@ -258,6 +268,7 @@ def _expand_glob_source(source_path: str, repo_path: str) -> list[str]:
     
     # Expand glob pattern
     matched = glob_module.glob(source_path, recursive=True)
+    total_matched = len(matched)
     
     # Filter to only paths within the repo and limit count
     results = []
@@ -266,7 +277,7 @@ def _expand_glob_source(source_path: str, repo_path: str) -> list[str]:
         if abs_path.startswith(os.path.abspath(repo_path)):
             results.append(abs_path)
         if len(results) >= MAX_GLOB_MATCHES:
-            logger.warning("Glob pattern matched too many files, limiting to %d", MAX_GLOB_MATCHES)
+            logger.warning("Glob pattern matched %d files, limited to %d", total_matched, MAX_GLOB_MATCHES)
             break
     
     return results
diff --git a/apps/api/src/models/config_profile.py b/apps/api/src/models/config_profile.py
index 1b5bc54..04eae6f 100644
--- a/apps/api/src/models/config_profile.py
+++ b/apps/api/src/models/config_profile.py
@@ -41,7 +41,7 @@ class ConfigProfile(UUIDPrimaryKeyMixin, TimestampMixin, Base):
     )  # {"rel/path": "content", ...}
     git_mounts: Mapped[list] = mapped_column(
         JSON, default=list, nullable=False
-    )  # [{"repo_id": "uuid", "source_path": ".", "target_path": "/path", "branch": "main"}, ...]
+    )  # [{"remote_url": "https://github.com/user/repo.git", "source_path": ".", "target_path": "/path", "branch": "main"}, ...]
     is_default: Mapped[bool] = mapped_column(Boolean, default=False, nullable=False)
 
     user: Mapped["User"] = relationship()
diff --git a/apps/api/tests/unit/test_git_mount_resolution.py b/apps/api/tests/unit/test_git_mount_resolution.py
index 9fbca4c..52b0b63 100644
--- a/apps/api/tests/unit/test_git_mount_resolution.py
+++ b/apps/api/tests/unit/test_git_mount_resolution.py
@@ -91,23 +91,22 @@ class TestCheckoutBranch:
         assert result == "feature"
 
     def test_checkout_nonexistent_branch(self, tmp_path: Path) -> None:
-        """Test checking out a non-existent branch raises error."""
+        """Test checking out a non-existent branch returns False."""
         os.system(f"cd {tmp_path} && git init && git config user.email 'test@test.com' && git config user.name 'Test'")
         (tmp_path / "file.txt").write_text("content")
         os.system(f"cd {tmp_path} && git add . && git commit -m 'initial'")
         
-        with pytest.raises(RuntimeError, match="Failed to checkout branch"):
-            _checkout_branch(str(tmp_path), "nonexistent")
+        result = _checkout_branch(str(tmp_path), "nonexistent")
+        assert result is False
 
 
 class TestResolveSingleGitMount:
     """Unit tests for resolving a single git mount."""
 
     @pytest.mark.asyncio
-    async def test_resolve_missing_repo(self, db_session) -> None:
-        """Test that missing repo returns empty list."""
+    async def test_resolve_missing_remote_url(self, db_session) -> None:
+        """Test that missing remote_url returns empty list."""
         git_mount = {
-            "repo_id": "12345678-1234-1234-1234-123456789abc",
             "source_path": ".",
             "target_path": "/app",
         }
@@ -119,21 +118,9 @@ class TestResolveSingleGitMount:
     async def test_resolve_missing_target_path(self, db_session) -> None:
         """Test that missing target path returns empty list."""
         git_mount = {
-            "repo_id": "12345678-1234-1234-1234-123456789abc",
+            "remote_url": "https://github.com/user/repo.git",
             "source_path": ".",
         }
         
         result = await _resolve_single_git_mount(db_session, git_mount)
         assert result == []
-
-    @pytest.mark.asyncio
-    async def test_resolve_invalid_repo_id(self, db_session) -> None:
-        """Test that invalid repo_id returns empty list."""
-        git_mount = {
-            "repo_id": "not-a-uuid",
-            "source_path": ".",
-            "target_path": "/app",
-        }
-        
-        result = await _resolve_single_git_mount(db_session, git_mount)
-        assert result == []