diff --git a/apps/api/src/services/tool/instance_service.py b/apps/api/src/services/tool/instance_service.py
index 1771893..39a368a 100644
--- a/apps/api/src/services/tool/instance_service.py
+++ b/apps/api/src/services/tool/instance_service.py
@@ -204,7 +204,12 @@ def clone_git_repo(
     """
     import hashlib
 
-    url_hash = hashlib.md5(remote_url.encode()).hexdigest()[:12]
+    # Include the branch in the hash so different branches of the same repo
+    # get separate clone directories and cannot race each other.
+    branch_segment = branch or "default"
+    url_hash = hashlib.md5(
+        f"{remote_url}:{branch_segment}".encode()
+    ).hexdigest()[:12]
     repo_name = remote_url.split("/")[-1].replace(".git", "") or "repo"
     clone_dir = os.path.join(clone_parent, "git-mounts", f"{repo_name}-{url_hash}")
     repo_path = os.path.join(clone_dir, "repo-clone")
@@ -303,8 +308,20 @@ def resolve_git_mount_mappings(
                 # Single match: mount directly to target_path
                 mount_target = final_target
             else:
-                # Multiple matches: append relative path to target
-                rel_path = os.path.relpath(matched_path, repo_path)
+                # Multiple matches: append the path relative to the glob's base
+                # directory so `packages/*` → `/app/packages` yields
+                # `/app/packages/api` instead of `/app/packages/packages/api`.
+                first_glob_idx = min(
+                    (source_path.find(c) for c in "*?[" if c in source_path),
+                    default=len(source_path),
+                )
+                base_relative = os.path.dirname(source_path[: first_glob_idx + 1])
+                base_full = (
+                    os.path.join(repo_path, base_relative)
+                    if base_relative
+                    else repo_path
+                )
+                rel_path = os.path.relpath(matched_path, base_full)
                 mount_target = os.path.join(final_target, rel_path)
 
             volume_mounts.append(
@@ -357,7 +374,14 @@ async def resolve_single_git_mount(
         repo_path = await asyncio.to_thread(
             clone_git_repo, remote_url, branch, instance_dir
         )
-    except Exception:
+    except Exception as exc:
+        logger.warning(
+            "Git mount clone failed for %s (branch=%s): %s",
+            remote_url,
+            branch,
+            exc,
+            exc_info=True,
+        )
         return []
 
     # Resolve all mappings from the cloned repo
@@ -1241,7 +1265,7 @@ async def start_tool_instance(
 
     # Fetch tool type early to determine home directory and container user
     tool_type = await session.get(ToolType, instance.tool_type_id)
-    home_dir = "/root"
+    home_dir = tool_type.home_directory if tool_type and tool_type.home_directory else "/root"
     container_uid = 0
     container_gid = 0
     if tool_type and tool_type.definition_type == "manifest" and tool_type.manifest_id:
@@ -1259,16 +1283,22 @@ async def start_tool_instance(
                         deep_merge(dict(base_def.manifest), manifest)
                     )
             home_dir = get_manifest_home_dir(manifest)
+            runtime = manifest.get("runtime", {})
+            if runtime.get("working_dir"):
+                working_directory = expand_container_path(
+                    runtime["working_dir"], home_dir
+                )
             user_cfg = manifest.get("user")
             if user_cfg:
                 container_uid = user_cfg.get("uid", 0)
                 container_gid = user_cfg.get("gid", 0)
             logger.debug(
-                "Manifest user resolved for instance %s: uid=%s, gid=%s, home=%s",
+                "Manifest user resolved for instance %s: uid=%s, gid=%s, home=%s, working_directory=%s",
                 instance.id,
                 container_uid,
                 container_gid,
                 home_dir,
+                working_directory,
             )
 
     # Apply selected config profile if any
@@ -1281,6 +1311,16 @@ async def start_tool_instance(
             profile_env, profile_files, profile_mounts, profile_hints = (
                 apply_resolved_profile(instance_dir, resolved, home_dir)
             )
+            # Profile hints override the manifest/tool defaults, and git mounts
+            # need the final working directory to resolve relative target paths.
+            if profile_hints.get("start_command"):
+                start_command = profile_hints["start_command"]
+            if profile_hints.get("working_directory"):
+                working_directory = expand_container_path(
+                    profile_hints["working_directory"], home_dir
+                )
+            if profile_hints.get("port_override"):
+                port_override = profile_hints["port_override"]
             env_vars.update(profile_env)
             config_files.update(profile_files)
             extra_volumes.extend(profile_mounts)
@@ -1288,12 +1328,6 @@ async def start_tool_instance(
                 session, resolved, instance_dir, working_directory, home_dir
             )
             extra_volumes.extend(git_mount_volumes)
-            if profile_hints.get("start_command"):
-                start_command = profile_hints["start_command"]
-            if profile_hints.get("working_directory"):
-                working_directory = profile_hints["working_directory"]
-            if profile_hints.get("port_override"):
-                port_override = profile_hints["port_override"]
             logger.debug(
                 "Applied config profile %s to instance %s (env=%d, files=%d, mounts=%d, git_mounts=%d)",
                 resolved.profile_name,