diff --git a/.gitignore b/.gitignore
index e0b5bf61..c97a382c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,11 +2,7 @@ target/
 experiment_outputs/
 asap-quickstart/bin/
 
-# Runtime and generated files
-metadata/
-preprocessed_configs/
-status
-uuid
-store/
 # roborev snapshots
 /.roborev/
+
+/.agent/
diff --git a/gwt.sh b/gwt.sh
index fd328bbe..86d33121 100755
--- a/gwt.sh
+++ b/gwt.sh
@@ -35,9 +35,10 @@ echo "Found branch: $branch_name"
 echo "Fetching from origin..."
 git fetch origin "$branch_name"
 
-echo "Creating worktree at ../worktrees/$issue_num..."
+echo "Creating worktree at .agent/worktrees/$branch_name..."
+mkdir -p .agent/worktrees
 if git show-ref --verify --quiet "refs/heads/$branch_name"; then
-  git worktree add "../worktrees/$issue_num" "$branch_name"
+  git worktree add ".agent/worktrees/$branch_name" "$branch_name"
 else
-  git worktree add --track -b "$branch_name" "../worktrees/$issue_num" "origin/$branch_name"
+  git worktree add --track -b "$branch_name" ".agent/worktrees/$branch_name" "origin/$branch_name"
 fi