From 0c9e172ce178764260cf1f43a614e2fd9ca67a42 Mon Sep 17 00:00:00 2001
From: Vojtech <119944107+cvrysanek@users.noreply.github.com>
Date: Tue, 19 May 2026 20:45:45 +0400
Subject: [PATCH] fix(init): chmod +x workspace hooks in OVERRIDE mode too
 (#359)
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`agnes init` ran `_chmod_workspace_hooks(workspace)` only in DEFAULT
mode (inside `if not override_active:`). The OVERRIDE path — used for
Initial-Workspace-Template seed-repo flows where the admin's template
repo is cloned into the workspace — silently skipped chmod.

When the seed repo's git checkout didn't preserve the +x bit
(filemode=false, archive extractions, FUSE/NFS mounts), hooks like
`.claude/hooks/skill-nudge/nudge.sh` and
`.claude/hooks/prompt-history/log-prompt.sh` landed non-executable
and every SessionStart fired `Permission denied`. The chmod helper
itself already recurses (`rglob`) so the subdir-scoped hook layouts
were covered — the bug was the call site.

Moved the call out of the override gate to a common step before the
first pull. Both DEFAULT and OVERRIDE paths now chmod hooks before
the first SessionStart can fire.
---
 CHANGELOG.md         | 15 +++++++++++++++
 cli/commands/init.py | 17 ++++++++++++++++-
 2 files changed, 31 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ae3fd5a..5d38c3e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,21 @@ CalVer image tags (`stable-YYYY.MM.N`, `dev-YYYY.MM.N`) are produced for every C
 
 ## [Unreleased]
 
+### Fixed
+- `agnes init` now runs `_chmod_workspace_hooks(workspace)` for OVERRIDE
+  mode too (Initial Workspace Template seed-repo flow), not just the
+  DEFAULT path. Override-mode workspaces seeded from an admin's
+  template repo were leaving hooks like
+  `.claude/hooks/skill-nudge/nudge.sh` and
+  `.claude/hooks/prompt-history/log-prompt.sh` non-executable when
+  the seed repo's git checkout didn't preserve the +x bit
+  (`core.filemode=false`, archive extractions, FUSE/NFS mounts), and
+  every SessionStart fired `Permission denied`. The chmod helper
+  already recurses (`rglob`) so subdir-scoped hook layouts were
+  covered — the bug was that the call site sat inside the
+  `if not override_active:` block. Moved out to a common step
+  before the first pull so every init path runs it.
+
 ## [0.55.4] — 2026-05-19
 
 ### Security
diff --git a/cli/commands/init.py b/cli/commands/init.py
index b35d555..dffe817 100644
--- a/cli/commands/init.py
+++ b/cli/commands/init.py
@@ -493,7 +493,6 @@ def init(
             ), encoding="utf-8")
         install_claude_hooks(workspace)
         install_claude_commands(workspace)
-        _chmod_workspace_hooks(workspace)
 
         # ------------------------------------------------------------------
         # Step 6: CLAUDE.local.md stub — only when absent. `--force` does NOT
@@ -511,6 +510,22 @@ def init(
                 encoding="utf-8",
             )
 
+    # ------------------------------------------------------------------
+    # Always chmod +x hook scripts that landed on disk, regardless of
+    # which path seeded the workspace. In DEFAULT mode the hooks come
+    # from `install_claude_hooks` above; in OVERRIDE mode they come
+    # from the admin's initial-workspace-template clone — and `git
+    # checkout` of that template doesn't reliably preserve the +x bit
+    # (filemode=false repos, archive extractions, FUSE/NFS mounts),
+    # so hooks like `.claude/hooks/skill-nudge/nudge.sh` or
+    # `.claude/hooks/prompt-history/log-prompt.sh` could land non-
+    # executable and fire `Permission denied` on the very next
+    # SessionStart. `_chmod_workspace_hooks` recurses (`rglob`) so
+    # subdir-scoped hook layouts are covered. Best-effort, no-op on
+    # Windows NTFS.
+    # ------------------------------------------------------------------
+    _chmod_workspace_hooks(workspace)
+
     # ------------------------------------------------------------------
     # Step 7: first pull. `run_pull` records per-stage failures inside
     # `result.errors` rather than raising for transient issues, so any