diff --git a/doc/DEVELOPING.md b/doc/DEVELOPING.md
index 7d98cd6d..7864b90e 100644
--- a/doc/DEVELOPING.md
+++ b/doc/DEVELOPING.md
@@ -206,6 +206,17 @@ paperclipai worktree init --from-data-dir ~/.paperclip
 paperclipai worktree init --force
 ```
 
+Repair an already-created repo-managed worktree and reseed its isolated instance from the main default install:
+
+```sh
+cd ~/.paperclip/worktrees/PAP-884-ai-commits-component
+pnpm paperclipai worktree init --force --seed-mode minimal \
+  --name PAP-884-ai-commits-component \
+  --from-config ~/.paperclip/instances/default/config.json
+```
+
+That rewrites the worktree-local `.paperclip/config.json` + `.paperclip/.env`, recreates the isolated instance under `~/.paperclip-worktrees/instances/<worktree-id>/`, and preserves the git worktree contents themselves.
+
 **`pnpm paperclipai worktree:make <name> [options]`** — Create `~/NAME` as a git worktree, then initialize an isolated Paperclip instance inside it. This combines `git worktree add` with `worktree init` in a single step.
 
 | Option | Description |
diff --git a/scripts/provision-worktree.sh b/scripts/provision-worktree.sh
index ea5e0e0f..19b0831e 100644
--- a/scripts/provision-worktree.sh
+++ b/scripts/provision-worktree.sh
@@ -32,13 +32,13 @@ source_env_path="$(dirname "$source_config_path")/.env"
 mkdir -p "$paperclip_dir"
 
 run_isolated_worktree_init() {
-  if command -v paperclipai >/dev/null 2>&1; then
-    paperclipai worktree init --force --name "$worktree_name" --from-config "$source_config_path"
+  if command -v pnpm >/dev/null 2>&1 && pnpm paperclipai --help >/dev/null 2>&1; then
+    pnpm paperclipai worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
     return 0
   fi
 
-  if command -v pnpm >/dev/null 2>&1 && pnpm paperclipai --help >/dev/null 2>&1; then
-    pnpm paperclipai worktree init --force --name "$worktree_name" --from-config "$source_config_path"
+  if command -v paperclipai >/dev/null 2>&1; then
+    paperclipai worktree init --force --seed-mode minimal --name "$worktree_name" --from-config "$source_config_path"
     return 0
   fi