refactor: use JSON file exchange instead of stdout parsing

Replace fragile patterns like:
  python3 -c "import json; print(json.load(...))" | grep
  echo "$json" | python3 -c "import sys,json; ...

.gitignore

@@ -4,3 +4,4 @@ results/
 */results/
 *.pyc
 
+.kugetsu/

skills/kugetsu/scripts/kugetsu-index.sh

@@ -139,6 +139,77 @@ validate_issue_ref() {
     fi
 }
 
+read_json_file() {
+    local file_path="$1"
+    if [ -f "$file_path" ]; then
+        cat "$file_path"
+    else
+        echo "{}"
+    fi
+}
+
+write_json_file() {
+    local file_path="$1"
+    local json_content="$2"
+    local temp_file="$file_path.tmp.$$"
+    
+    printf '%s' "$json_content" > "$temp_file"
+    
+    if ! python3 -c "import json; json.load(open('$temp_file'))" 2>/dev/null; then
+        echo "Error: write_json_file would create malformed JSON: $file_path" >&2
+        rm -f "$temp_file"
+        return 1
+    fi
+    
+    mv "$temp_file" "$file_path"
+}
+
+get_json_value() {
+    local file_path="$1"
+    local key="$2"
+    local default="${3:-}"
+    
+    if [ ! -f "$file_path" ]; then
+        echo "$default"
+        return
+    fi
+    
+    python3 -c "import json; print(json.load(open('$file_path')).get('$key', '$default'))" 2>/dev/null || echo "$default"
+}
+
+set_json_value() {
+    local file_path="$1"
+    local key="$2"
+    local value="$3"
+    
+    if [ ! -f "$file_path" ]; then
+        printf '{"%s": "%s"}\n' "$key" "$value" > "$file_path"
+        return
+    fi
+    
+    python3 << PYEOF
+import json
+import sys
+
+file_path = "$file_path"
+key = "$key"
+value = "$value"
+
+try:
+    with open(file_path, 'r') as f:
+        data = json.load(f)
+except:
+    data = {}
+
+data[key] = value
+
+with open(file_path, 'w') as f:
+    json.dump(data, f, indent=2)
+
+print(f"Set $key = $value in $file_path")
+PYEOF
+}
+
 update_session_pr_url() {
     local issue_ref="$1"
     local pr_url="$2"

skills/kugetsu/scripts/kugetsu-queue-daemon.sh

@@ -34,6 +34,8 @@ release_lock() {
 check_task_completion() {
     local item="$1"
     local queue_id=$(basename "$item" .json)
+    
+    local item_data=$(read_json_file "$item")
     local state=$(python3 -c "import json; print(json.load(open('$item')).get('state', ''))" 2>/dev/null)
 
     [ "$state" = "notified" ] || return 0
@@ -41,6 +43,31 @@ check_task_completion() {
     local session_id=$(python3 -c "import json; print(json.load(open('$item')).get('opencode_session_id', ''))" 2>/dev/null)
     local issue_ref=$(python3 -c "import json; print(json.load(open('$item')).get('issue_ref', ''))" 2>/dev/null)
     local pid=$(python3 -c "import json; print(json.load(open('$item')).get('pid', ''))" 2>/dev/null)
+    local notified_at=$(python3 -c "import json; print(json.load(open('$item')).get('notified_at', ''))" 2>/dev/null)
+
+    local timed_out=false
+    if [ -n "$notified_at" ]; then
+        local notified_epoch=$(date -d "$notified_at" +%s 2>/dev/null || echo "0")
+        local now_epoch=$(date +%s)
+        local hours_elapsed=$(( (now_epoch - notified_epoch) / 3600 ))
+        if [ "$hours_elapsed" -ge "${TASK_TIMEOUT_HOURS:-1}" ]; then
+            timed_out=true
+            log_warn "queue-daemon" "Task $queue_id ($issue_ref) timed out after ${hours_elapsed}h"
+        fi
+    fi
+
+    if [ "$timed_out" = true ]; then
+        if [ -n "$pid" ] && [ "$pid" != "None" ]; then
+            kill "$pid" 2>/dev/null || true
+        fi
+        if [ -n "$session_id" ]; then
+            opencode session stop "$session_id" 2>/dev/null || true
+        fi
+        update_queue_item_state "$queue_id" "error"
+        log_error "queue-daemon" "Task $queue_id ($issue_ref) marked error — timeout after ${hours_elapsed}h"
+        release_lock "$issue_ref"
+        return
+    fi
 
     if [ -n "$pid" ] && [ "$pid" != "None" ]; then
         if ! kill -0 "$pid" 2>/dev/null; then

skills/kugetsu/scripts/kugetsu-session.sh

@@ -239,23 +239,34 @@ create_session() {
         return 1
     fi
     
-    local before_json=$(opencode session list --format=json 2>/dev/null)
+    local before_file="$KUGETSU_DIR/sessions/before$$.json"
-    local before_set=$(echo "$before_json" | python3 -c "import sys,json; sessions=json.load(sys.stdin); print('|'.join(s['id'] for s in sessions))" 2>/dev/null || echo "|")
+    local after_file="$KUGETSU_DIR/sessions/after$$.json"
+    
+    opencode session list --format=json > "$before_file" 2>/dev/null || printf '{}' > "$before_file"
     
     opencode run --fork --session "$base_session" "new session" >/dev/null 2>&1
     
     sleep 1
     
-    local after_json=$(opencode session list --format=json 2>/dev/null)
+    opencode session list --format=json > "$after_file" 2>/dev/null || printf '{}' > "$after_file"
-    local after_sessions=$(echo "$after_json" | python3 -c "import sys,json; sessions=json.load(sys.stdin); [print(s['id']) for s in sessions]" 2>/dev/null || true)
     
-    local new_session_id=""
+    local new_session_id=$(python3 << PYEOF
-    while IFS= read -r sess; do
+import json
-        if [[ -n "$sess" ]] && [[ ! "$before_set" =~ \|${sess}\| ]]; then
+
-            new_session_id="$sess"
+with open("$before_file", 'r') as f:
-            break
+    before = json.load(f)
-        fi
+with open("$after_file", 'r') as f:
-    done <<< "$after_sessions"
+    after = json.load(f)
+
+before_ids = set(s['id'] for s in before)
+for s in after:
+    if s['id'] not in before_ids:
+        print(s['id'])
+        break
+PYEOF
+)
+    
+    rm -f "$before_file" "$after_file"
     
     echo "$new_session_id"
 }
@@ -270,40 +281,37 @@ build_dev_agent_message() {
     local number=$(echo "$issue_ref" | grep -oE '#[0-9]+$' | tr -d '#')
     local worktree_path=$(issue_ref_to_worktree_path "$issue_ref")
     
+    local conflict_check=""
+    local review_notes=""
+    local delegator_header=""
+    local delegator_footer=""
     if [ -n "$user_message" ]; then
-        cat <<EOF
+        conflict_check="   - CRITICAL: Check if PR has merge conflicts before asking for review:
-You are continuing work on $issue_ref. A PR likely already exists.
+     - Use: curl -s \"https://$instance/api/v1/repos/$owner/$repo/pulls/$number\" -H \"Authorization: Bearer \$GITEA_TOKEN\"
+     - If \"mergeable\": false, there ARE conflicts - you MUST resolve them FIRST
+     - To resolve: cd to worktree, git fetch origin, git rebase origin/main, resolve conflicts, git rebase --continue, git push --force-with-lease
+     - Only after resolving conflicts (mergeable: true) can you ask for review"
+        delegator_header="IMPORTANT: Follow the workflow below as your guideline, but prioritize the delegator's message.
 
-IMPORTANT - Review workflow:
+Workflow:"
-1. First, check if PR exists: curl -s "https://$instance/api/v1/repos/$owner/$repo/pulls?state=open" -H "Authorization: Bearer \$GITEA_TOKEN" | grep -i "$number"
+        delegator_footer="
-2. Get PR comments: curl -s "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN"
-3. Get PR reviews: curl -s "https://$instance/api/v1/repos/$owner/$repo/pulls/$number/reviews" -H "Authorization: Bearer \$GITEA_TOKEN"
-
-You may need to:
-- Make code changes and push to the same branch
-- Reply to PR comments using: curl -X POST "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN" -H "Content-Type: application/json" -d '{"body":"Your reply here"}'
-- Or do both
-
-MERGING: If instructed to merge, you MUST confirm approval first before merging:
-- Check for PR approval via: curl -s "https://$instance/api/v1/repos/$owner/$repo/pulls/$number/reviews" -H "Authorization: Bearer \$GITEA_TOKEN"
-- Check for "lgtm" or "approved" in comments: curl -s "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN"
-- Only merge if you see approval OR the instruction explicitly says to merge (e.g., "merge the PR", "please merge", "go ahead and merge")
-- To merge: tea pr merge --repo $owner/$repo $number --style merge
-- If no approval yet, reply asking for review/approval first
 
 Delegator's message:
-$user_message
+$user_message"
-
-Work directory: $worktree_path (already on the fix branch)
-EOF
     else
-        cat <<EOF
+        review_notes="  - IMPORTANT: After listing reviews, READ the review comments and incorporate feedback
+  - Check for review state: \"APPROVED\" means ready to merge, \"COMMENT\" means feedback to address"
+        delegator_header="Workflow:"
+    fi
+    
+    cat <<EOF
 You are assigned to work on $issue_ref.
 
-Workflow:
+$delegator_header
 1. Read the issue at $instance/$owner/$repo/issues/$number AND all comments on that issue
 2. Check if a PR already exists for this issue
    - If PR exists and is open, review it and learn from it
+$conflict_check
    - If PR makes sense to continue, work on it instead
    - If PR is not worth continuing, create a new branch/PR but explain in PR description why you're creating a new one instead of continuing the existing PR
 3. Read README.md (if exists) to understand the general concept of this repository
@@ -321,13 +329,14 @@ Tools for PR interaction:
 - Post issue/PR comment: curl -X POST "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN" -H "Content-Type: application/json" -d '{"body":"Your comment"}'
 - List PR comments: curl -s "https://$instance/api/v1/repos/$owner/$repo/issues/$number/comments" -H "Authorization: Bearer \$GITEA_TOKEN"
 - List PR reviews: curl -s "https://$instance/api/v1/repos/$owner/$repo/pulls/$number/reviews" -H "Authorization: Bearer \$GITEA_TOKEN"
+$review_notes
 - Merge PR (only with approval): tea pr merge --repo $owner/$repo $number --style merge
   - MERGING requires approval first! Check for: approval in reviews, OR "lgtm"/"approved" in comments
   - If no approval, ask reviewer to approve first before merging
+$delegator_footer
 
 Work directory: $worktree_path
 EOF
-    fi
 }
 
 ensure_worktree() {
@@ -386,12 +395,6 @@ ensure_session() {
         return 0
     fi
     
-    if $worktree_exists && ! $session_exists; then
-        log "warn" "ensure_session" "Worktree exists but session is missing. Removing worktree to recreate both..."
-        remove_worktree_for_issue "$issue_ref"
-        worktree_exists=false
-    fi
-    
     if ! $worktree_exists && $session_exists; then
         log "warn" "ensure_session" "Session exists but worktree is missing. Removing stale session..."
         rm -f "$session_path"
@@ -481,6 +484,8 @@ cmd_continue() {
     
     if [ -z "$message" ]; then
         message=$(build_dev_agent_message "$issue_ref" "")
+    else
+        message=$(build_dev_agent_message "$issue_ref" "$message")
     fi
     
     local worktree_status=$(ensure_worktree "$issue_ref")
@@ -495,6 +500,8 @@ cmd_continue() {
         exit 1
     fi
     
+    kugetsu_context_dump "$issue_ref" "$message" "$(issue_ref_to_branch_name "$issue_ref")"
+    
     local session_file=$(issue_ref_to_filename "$issue_ref")
     local session_path="$SESSIONS_DIR/$session_file"
     local opencode_session_id=$(python3 -c "import json; print(json.load(open('$session_path')).get('opencode_session_id', ''))" 2>/dev/null || echo "")

skills/kugetsu/scripts/kugetsu-worktree.sh

@@ -145,15 +145,17 @@ check_pr_status() {
         token="${GITEA_TOKEN:-}"
     fi
     
-    local response
+    local response_file="$KUGETSU_DIR/.pr_status_response_$$.json"
     if [ -n "$token" ]; then
-        response=$(curl -s -H "Authorization: token $token" "$api_url" 2>/dev/null || echo "{}")
+        curl -s -H "Authorization: token $token" "$api_url" > "$response_file" 2>/dev/null || printf '{}' > "$response_file"
     else
-        response=$(curl -s "$api_url" 2>/dev/null || echo "{}")
+        curl -s "$api_url" > "$response_file" 2>/dev/null || printf '{}' > "$response_file"
     fi
     
-    local state=$(echo "$response" | python3 -c "import json, sys; d=json.load(sys.stdin); print(d.get('state', 'unknown'))" 2>/dev/null || echo "unknown")
+    local state=$(python3 -c "import json; print(json.load(open('$response_file')).get('state', 'unknown'))" 2>/dev/null || echo "unknown")
-    local merged=$(echo "$response" | python3 -c "import json, sys; d=json.load(sys.stdin); print('true' if d.get('merged', False) else 'false')" 2>/dev/null || echo "false")
+    local merged=$(python3 -c "import json; print('true' if json.load(open('$response_file')).get('merged', False) else 'false')" 2>/dev/null || echo "false")
+    
+    rm -f "$response_file"
     
     if [ "$merged" = "true" ]; then
         echo "merged"