From ca9c73da0f82af2b22fb1ea6c3140f9a858708a5 Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Mon, 23 Mar 2026 12:18:57 -0500
Subject: [PATCH] docs: explain extension file overlap in finalize_setup scan
 comment

---
 src/specify_cli/agent_pack.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/specify_cli/agent_pack.py b/src/specify_cli/agent_pack.py
index 4786c6fe9..7899fba6e 100644
--- a/src/specify_cli/agent_pack.py
+++ b/src/specify_cli/agent_pack.py
@@ -383,6 +383,12 @@ class AgentBootstrap:
         # (e.g. .claude/) so we catch both commands and skills
         # directories (skills-migrated agents replace the commands
         # directory with a sibling skills directory during init).
+        #
+        # Note: extension command files live under agent_root too, so
+        # they may appear in both agent_files and extension_files.
+        # This is harmless — during teardown the two dicts are merged
+        # by key ({**agent, **ext}), so duplicates are deduplicated
+        # and the hash is identical either way.
         if self.manifest.commands_dir:
             agent_root = self.agent_dir(project_path)
             if agent_root.is_dir():