From 38ae7595685ae9a216f531a538066af0aadd7dfe Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Mon, 23 Mar 2026 12:44:25 -0500
Subject: [PATCH] fix: stale manifest cleanup, resolve with project_path,
 AGENTS.md add docs

- remove_tracked_files: count only still-existing files as remaining;
  user-deleted files no longer prevent manifest cleanup
- init --agent: pass project_path to resolve_agent_pack so project-level
  overrides (.specify/agents/) are honored during --here init
- AGENTS.md: update agent add to show --from <path> requirement and note
  catalog fetch is not yet implemented
---
 AGENTS.md                     |  4 +++-
 src/specify_cli/__init__.py   |  2 +-
 src/specify_cli/agent_pack.py | 15 ++++++++++-----
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/AGENTS.md b/AGENTS.md
index 6fc9303f1..664418dea 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -453,9 +453,11 @@ specify init --here --agent gemini --ai-skills  # With skills
 | `specify agent search [query]`  | Search agents by name, ID, description, or tags |
 | `specify agent validate <path>` | Validate an agent pack directory |
 | `specify agent export <id>`     | Export an agent pack for editing |
-| `specify agent add <id>`        | Install an agent pack from a local path |
+| `specify agent add <id> --from <path>` | Install an agent pack from a local directory |
 | `specify agent remove <id>`     | Remove a cached/override agent pack |
 
+> **Note:** `specify agent add <id>` without `--from <path>` is reserved for future catalog-based installation, which is not yet implemented.
+
 ### Pack resolution order
 
 Agent packs resolve by priority (highest first):
diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index ea432804b..f4378e743 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1877,7 +1877,7 @@ def init(
     if use_agent_pack:
         from .agent_pack import resolve_agent_pack, load_bootstrap, PackResolutionError, AgentPackError
         try:
-            resolved = resolve_agent_pack(selected_ai)
+            resolved = resolve_agent_pack(selected_ai, project_path=project_path)
             agent_bootstrap = load_bootstrap(resolved.path, resolved.manifest)
             console.print(f"[dim]Pack-based flow: {resolved.manifest.name} ({resolved.source})[/dim]")
         except (PackResolutionError, AgentPackError) as exc:
diff --git a/src/specify_cli/agent_pack.py b/src/specify_cli/agent_pack.py
index 7899fba6e..d77404bf2 100644
--- a/src/specify_cli/agent_pack.py
+++ b/src/specify_cli/agent_pack.py
@@ -695,12 +695,17 @@ def remove_tracked_files(
             abs_path.unlink()
             removed.append(rel_path)
 
-    # Clean up the install manifest only when all tracked files were
-    # removed.  If some were skipped (modified), keep the manifest so
-    # those files remain tracked for future teardown attempts.
+    # Clean up the install manifest only when no tracked files remain
+    # on disk.  Files already deleted by the user count as gone, not
+    # as "remaining" — only files that still exist and were skipped
+    # (e.g. modified without --force) prevent manifest cleanup.
     if manifest_file.is_file():
-        remaining = len(entries) - len(removed)
-        if remaining == 0:
+        still_on_disk = sum(
+            1 for rel_path in entries
+            if (project_path / rel_path).is_file()
+            and rel_path not in removed
+        )
+        if still_on_disk == 0:
             manifest_file.unlink(missing_ok=True)
     return removed