fix(commands): use background Bash to avoid shell timeout killing servers

Replace ! preprocessing with run_in_background Bash instructions in review, annotate, and annotate-last commands. The ! syntax blocks on waitForDecision() which exceeds the ~120s shell timeout, killing the server and losing unsaved annotations.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: Alex Doan

apps/hook/commands/plannotator-annotate.md

@@ -4,9 +4,11 @@ allowed-tools: Bash(plannotator:*)
 disable-model-invocation: true
 ---
 
-## Markdown Annotations
+## Instructions
 
-!`plannotator annotate $ARGUMENTS`
+Run `plannotator annotate $ARGUMENTS` using the Bash tool with `run_in_background: true`. This starts an annotation server and opens the browser. The user will annotate the document and submit feedback — this may take a long time.
+
+**Wait for the background task to complete before proceeding.** Do not interrupt or take other actions while the user is annotating.
 
 ## Your task
 

apps/hook/commands/plannotator-last.md

@@ -4,9 +4,11 @@ allowed-tools: Bash(plannotator:*)
 disable-model-invocation: true
 ---
 
-## Message Annotations
+## Instructions
 
-!`plannotator annotate-last $ARGUMENTS`
+Run `plannotator annotate-last $ARGUMENTS` using the Bash tool with `run_in_background: true`. This starts an annotation server and opens the browser. The user will annotate the message and submit feedback — this may take a long time.
+
+**Wait for the background task to complete before proceeding.** Do not interrupt or take other actions while the user is annotating.
 
 ## Your task
 

apps/hook/commands/plannotator-review.md

@@ -4,10 +4,12 @@ allowed-tools: Bash(plannotator:*)
 disable-model-invocation: true
 ---
 
-## Code Review Feedback
+## Instructions
 
-!`plannotator review $ARGUMENTS`
+Run `plannotator review $ARGUMENTS` using the Bash tool with `run_in_background: true`. This starts a review server and opens the browser. The user will review code and submit feedback — this may take a long time.
+
+**Wait for the background task to complete before proceeding.** Do not interrupt or take other actions while the user is reviewing.
 
 ## Your task
 
-If the review above contains feedback or annotations, address them. If no changes were requested, acknowledge and continue.
+When the command finishes, read its output. If it contains feedback or annotations, address them. If no changes were requested, acknowledge and continue.