diff --git a/docs/fish-config.md b/docs/fish-config.md
index 232c735..ee6f848 100644
--- a/docs/fish-config.md
+++ b/docs/fish-config.md
@@ -1148,9 +1148,13 @@ Add -i (interactive confirmation) to destructive commands:
     every commit: MINOR (resetting PATCH) when the tracked directory set
     changes, PATCH otherwise; MAJOR is manual-only. A prepare-commit-msg hook
     appends "(vX.Y.Z)" to the commit subject. Downstream tooling can read
-    AGENTS/.version - a changed MINOR field signals a structure change. The
-    script and hooks are shipped from scripts/agents-tools/ and refreshed when
-    their version marker is stale.
+    AGENTS/.version - a changed MINOR field signals a structure change. Because
+    core.hooksPath is a single setting, the local override would otherwise
+    shadow your global hooks; after bumping the version, each shim chains
+    (execs) to the global/system core.hooksPath hook of the same name so global
+    pre-commit / prepare-commit-msg hooks (e.g. ggshield, Git LFS) still run.
+    The script and hooks are shipped from scripts/agents-tools/ and refreshed
+    when their version marker is stale.
 
     agents-init
     agents-init --agents
diff --git a/functions/agents-init.fish b/functions/agents-init.fish
index bca1ba4..a44acfe 100644
--- a/functions/agents-init.fish
+++ b/functions/agents-init.fish
@@ -36,8 +36,11 @@
 #   core.hooksPath: a pre-commit hook bumps AGENTS/.version on every commit
 #   (MINOR when the tracked directory set changes, PATCH otherwise; MAJOR is
 #   manual-only), and a prepare-commit-msg hook appends "(vX.Y.Z)" to the
-#   commit subject. The script/hooks are version-managed from
-#   scripts/agents-tools/ and refreshed when their marker is stale.
+#   commit subject. Each shim then chains (execs) to the global/system
+#   core.hooksPath hook of the same name, so this local override does not
+#   shadow global hooks (e.g. ggshield, Git LFS). The script/hooks are
+#   version-managed from scripts/agents-tools/ and refreshed when their marker
+#   is stale.
 #
 #   With no flags, runs both --agents and --plugins setup. At the end of
 #   every invocation, commits any uncommitted changes in the AGENTS/ sub-repo
diff --git a/scripts/agents-tools/hooks/pre-commit b/scripts/agents-tools/hooks/pre-commit
index ff3f604..687879c 100755
--- a/scripts/agents-tools/hooks/pre-commit
+++ b/scripts/agents-tools/hooks/pre-commit
@@ -1,7 +1,18 @@
 #!/usr/bin/env bash
-# agents-tools-version: 1
-# Delegates to the repo's committed .agents-tools/version-bump. Guarded so a
-# missing script or failed rev-parse never blocks the commit (always exit 0).
+# agents-tools-version: 2
+# Runs the committed .agents-tools/version-bump, then chains to the user's
+# global/system git hook (core.hooksPath) so ggshield, LFS, etc. still run.
+# agents-init's local core.hooksPath override would otherwise shadow them.
+# Guarded so a missing script or failed rev-parse never blocks the commit;
+# only the chained global hook can fail it.
 root="$(git rev-parse --show-toplevel 2>/dev/null)" || exit 0
 [ -x "$root/.agents-tools/version-bump" ] && "$root/.agents-tools/version-bump" precommit
+
+# Chain to the global/system hook this local override is shadowing.
+global_hooks="$(git config --global core.hooksPath 2>/dev/null)"
+[ -z "$global_hooks" ] && global_hooks="$(git config --system core.hooksPath 2>/dev/null)"
+if [ -n "$global_hooks" ]; then
+  global_hooks="${global_hooks/#\~/$HOME}" # git stores ~ verbatim
+  [ -x "$global_hooks/pre-commit" ] && exec "$global_hooks/pre-commit" "$@"
+fi
 exit 0
diff --git a/scripts/agents-tools/hooks/prepare-commit-msg b/scripts/agents-tools/hooks/prepare-commit-msg
index 57aed4a..161ac70 100755
--- a/scripts/agents-tools/hooks/prepare-commit-msg
+++ b/scripts/agents-tools/hooks/prepare-commit-msg
@@ -1,7 +1,18 @@
 #!/usr/bin/env bash
-# agents-tools-version: 1
-# Delegates to the repo's committed .agents-tools/version-bump. Guarded so a
-# missing script or failed rev-parse never blocks the commit (always exit 0).
+# agents-tools-version: 2
+# Runs the committed .agents-tools/version-bump, then chains to the user's
+# global/system git hook (core.hooksPath) so any global prepare-commit-msg
+# still runs. agents-init's local core.hooksPath override would otherwise
+# shadow it. Guarded so a missing script or failed rev-parse never blocks the
+# commit; only the chained global hook can fail it.
 root="$(git rev-parse --show-toplevel 2>/dev/null)" || exit 0
 [ -x "$root/.agents-tools/version-bump" ] && "$root/.agents-tools/version-bump" prepmsg "$1"
+
+# Chain to the global/system hook this local override is shadowing.
+global_hooks="$(git config --global core.hooksPath 2>/dev/null)"
+[ -z "$global_hooks" ] && global_hooks="$(git config --system core.hooksPath 2>/dev/null)"
+if [ -n "$global_hooks" ]; then
+  global_hooks="${global_hooks/#\~/$HOME}" # git stores ~ verbatim
+  [ -x "$global_hooks/prepare-commit-msg" ] && exec "$global_hooks/prepare-commit-msg" "$@"
+fi
 exit 0
diff --git a/scripts/agents-tools/version-bump b/scripts/agents-tools/version-bump
index 72a950a..62dd023 100755
--- a/scripts/agents-tools/version-bump
+++ b/scripts/agents-tools/version-bump
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# agents-tools-version: 1
+# agents-tools-version: 2
 # Copyright (C) 2026 Rootiest
 # SPDX-License-Identifier: AGPL-3.0-or-later
 #