fix: add PR merge conflict check to dev agent workflow

Dev agent should check if PR has merge conflicts before asking for review.
This prevents approving a PR that has conflicts, which could introduce
new errors after rebase.

Changes:
- Add conflict check step in workflow for both with/without user message cases
- Use mergeable field from PR API to detect conflicts
- Instructions to rebase and resolve conflicts if mergeable: false

.gitignore

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

skills/kugetsu/scripts/kugetsu-config.sh

@@ -26,9 +26,6 @@ QUEUE_DAEMON_INTERVAL_MINUTES="${QUEUE_DAEMON_INTERVAL_MINUTES:-5}"
 QUEUE_CLEANUP_AGE_DAYS="${QUEUE_CLEANUP_AGE_DAYS:-7}"
 TASK_TIMEOUT_HOURS="${TASK_TIMEOUT_HOURS:-1}"
 
-NETWORK_RETRY_ATTEMPTS="${NETWORK_RETRY_ATTEMPTS:-3}"
-NETWORK_RETRY_DELAY_SECONDS="${NETWORK_RETRY_DELAY_SECONDS:-5}"
-
 # Load user config overrides (~/.kugetsu/config)
 if [ -f "$KUGETSU_DIR/config" ]; then
     source "$KUGETSU_DIR/config"
@@ -90,24 +87,3 @@ set_debug_mode() {
     
     echo "${filtered_args[@]}"
 }
-
-retry_with_backoff() {
-    local max_attempts="${1:-$NETWORK_RETRY_ATTEMPTS}"
-    local delay_seconds="${2:-$NETWORK_RETRY_DELAY_SECONDS}"
-    local command="$3"
-    local remaining_attempts=$max_attempts
-    
-    while [ $remaining_attempts -gt 0 ]; do
-        if eval "$command"; then
-            return 0
-        fi
-        remaining_attempts=$((remaining_attempts - 1))
-        if [ $remaining_attempts -gt 0 ]; then
-            log "warn" "retry_with_backoff" "Command failed, $remaining_attempts retries remaining. Waiting ${delay_seconds}s..."
-            sleep "$delay_seconds"
-            delay_seconds=$((delay_seconds * 2))
-        fi
-    done
-    log "error" "retry_with_backoff" "Command failed after $max_attempts attempts"
-    return 1
-}

skills/kugetsu/scripts/kugetsu-index.sh

@@ -139,77 +139,6 @@ 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

@@ -34,8 +34,6 @@ 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)
 
     [ "$state" = "notified" ] || return 0
@@ -43,31 +41,6 @@ check_task_completion() {
     local session_id=$(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

@@ -13,8 +13,7 @@ count_active_dev_sessions() {
     if [ -d "$SESSIONS_DIR" ]; then
         for session_file in "$SESSIONS_DIR"/*.json; do
             if [ -f "$session_file" ]; then
-                local filename
-                filename=$(basename "$session_file")
+                local filename=$(basename "$session_file")
                 if [ "$filename" != "base.json" ] && [ "$filename" != "pm-agent.json" ]; then
                     count=$((count + 1))
                 fi
@@ -240,55 +239,23 @@ create_session() {
         return 1
     fi
     
-    local before_file
-    before_file="$KUGETSU_DIR/sessions/before$$.json"
-    local after_file
-    after_file="$KUGETSU_DIR/sessions/after$$.json"
+    local before_json=$(opencode session list --format=json 2>/dev/null)
+    local before_set=$(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 "|")
     
-    opencode session list --format=json > "$before_file" 2>/dev/null || printf '{}' > "$before_file"
-    
-    local fork_success=false
-    local attempt=0
-    local max_attempts="${NETWORK_RETRY_ATTEMPTS:-3}"
-    
-    while [ $attempt -lt $max_attempts ] && [ "$fork_success" = false ]; do
-        attempt=$((attempt + 1))
-        if opencode run --fork --session "$base_session" "new session" >/dev/null 2>&1; then
-            fork_success=true
-        elif [ $attempt -lt $max_attempts ]; then
-            log "warn" "create_session" "Fork attempt $attempt failed, retrying..."
-            sleep "$((attempt * 2))"
-        fi
-    done
-    
-    if [ "$fork_success" = false ]; then
-        log "error" "create_session" "Failed to fork session after $max_attempts attempts"
-        rm -f "$before_file" "$after_file"
-        return 1
-    fi
+    opencode run --fork --session "$base_session" "new session" >/dev/null 2>&1
     
     sleep 1
     
-    opencode session list --format=json > "$after_file" 2>/dev/null || printf '{}' > "$after_file"
+    local after_json=$(opencode session list --format=json 2>/dev/null)
+    local after_sessions=$(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
-    new_session_id=$(python3 << PYEOF
-import json
-
-with open("$before_file", 'r') as f:
-    before = json.load(f)
-with open("$after_file", 'r') as f:
-    after = json.load(f)
-
-before_ids = set(s['id'] for s in before)
-for s in after:
-    if s['id'] not in before_ids:
-        print(s['id'])
-        break
-PYEOF
-)
-    
-    rm -f "$before_file" "$after_file"
+    local new_session_id=""
+    while IFS= read -r sess; do
+        if [[ -n "$sess" ]] && [[ ! "$before_set" =~ \|${sess}\| ]]; then
+            new_session_id="$sess"
+            break
+        fi
+    done <<< "$after_sessions"
     
     echo "$new_session_id"
 }
@@ -303,37 +270,21 @@ build_dev_agent_message() {
     local number=$(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 "$user_message" ]; then
-        conflict_check="   - CRITICAL: Check if PR has merge conflicts before asking for review:
-     - Use: curl -s \"https://$instance/api/v1/repos/$owner/$repo/pulls/$number\" -H \"Authorization: Bearer \$GITEA_TOKEN\"
-     - If \"mergeable\": false, there ARE conflicts - you MUST resolve them FIRST
-     - To resolve: cd to worktree, git fetch origin, git rebase origin/main, resolve conflicts, git rebase --continue, git push --force-with-lease
-     - Only after resolving conflicts (mergeable: true) can you ask for review"
-        delegator_header="IMPORTANT: Follow the workflow below as your guideline, but prioritize the delegator's message.
-
-Workflow:"
-        delegator_footer="
-
-Delegator's message:
-$user_message"
-    else
-        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
+        cat <<EOF
 You are assigned to work on $issue_ref.
 
-$delegator_header
+IMPORTANT: Follow the workflow below as your guideline, but prioritize the delegator's message.
+
+Workflow:
 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
-$conflict_check
+   - CRITICAL: Check if PR has merge conflicts before asking for review:
+     - Use: curl -s "https://$instance/api/v1/repos/$owner/$repo/pulls/$number" -H "Authorization: Bearer \$GITEA_TOKEN"
+     - If "mergeable": false, there ARE conflicts - you MUST resolve them FIRST
+     - To resolve: cd to worktree, git fetch origin, git rebase origin/main, resolve conflicts, git rebase --continue, git push --force-with-lease
+     - Only after resolving conflicts (mergeable: true) can you ask for review
    - If PR makes sense to continue, work on it instead
    - If PR is not worth continuing, create a new branch/PR but explain in PR description why you're creating a new one instead of continuing the existing PR
 3. Read README.md (if exists) to understand the general concept of this repository
@@ -351,14 +302,52 @@ Tools for PR interaction:
 - Post issue/PR comment: curl -X POST "https://$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
+
+Delegator's message:
+$user_message
 
 Work directory: $worktree_path
 EOF
+    else
+        cat <<EOF
+You are assigned to work on $issue_ref.
+
+Workflow:
+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
+   - CRITICAL: Check if PR has merge conflicts before asking for review:
+     - 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
+   - 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
+4. Read CONTRIBUTING.md (if exists) to understand how to contribute
+   - If CONTRIBUTING.md doesn't exist, follow steps 5-9 as your guideline
+5. Explore the repository to understand the codebase
+6. If anything is unclear, post a comment on the issue asking for clarification before implementing
+7. Implement the solution
+8. Create a branch named fix/issue-$number and implement the fix
+9. Create a PR when the implementation is complete using: tea pr create --repo $owner/$repo --title "Your PR title" --body "PR description"
+   - Make sure you are logged in with: tea login add --name gitea --token \$GITEA_TOKEN --url https://$instance
+   - If tea is not available, use: curl -X POST "https://$instance/api/v1/repos/$owner/$repo/pulls" -H "Authorization: Bearer \$GITEA_TOKEN" -H "Content-Type: application/json" -d '{"title":"PR Title","head":"branch-name","base":"main","body":"PR description"}'
+
+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"
+- 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
+
+Work directory: $worktree_path
+EOF
+    fi
 }
 
 ensure_worktree() {
@@ -411,20 +400,20 @@ ensure_session() {
         session_exists=true
     fi
     
-    if [ "$worktree_exists" = true ] && [ "$session_exists" = true ]; then
+    if $worktree_exists && $session_exists; then
         log "info" "ensure_session" "Session already exists for $issue_ref"
         echo "continued"
         return 0
     fi
     
-    if [ "$worktree_exists" = false ] && [ "$session_exists" = true ]; then
+    if ! $worktree_exists && $session_exists; then
         log "warn" "ensure_session" "Session exists but worktree is missing. Removing stale session..."
         rm -f "$session_path"
         remove_issue_from_index "$issue_ref"
         session_exists=false
     fi
     
-    if [ "$worktree_exists" = false ]; then
+    if ! $worktree_exists; then
         local wt_status=$(ensure_worktree "$issue_ref")
         if [ "$wt_status" != "created" ] && [ "$wt_status" != "existed" ]; then
             log "error" "ensure_session" "Failed to ensure worktree for $issue_ref"
@@ -522,8 +511,6 @@ 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

@@ -76,8 +76,7 @@ create_worktree() {
         exit 1
     fi
     
-    local worktree_parent_dir
-    worktree_parent_dir=$(dirname "$worktree_path")
+    local worktree_parent_dir=$(dirname "$worktree_path")
     mkdir -p "$worktree_parent_dir"
     
     if worktree_exists "$issue_ref" "$parent_dir"; then
@@ -86,36 +85,15 @@ create_worktree() {
     fi
     
     echo "Creating worktree at '$worktree_path'..."
-    
-    local clone_success=false
-    local attempt=0
-    local max_attempts="${NETWORK_RETRY_ATTEMPTS:-3}"
-    
-    while [ $attempt -lt $max_attempts ] && [ "$clone_success" = false ]; do
-        attempt=$((attempt + 1))
-        if [ $attempt -gt 1 ]; then
-            echo "Clone attempt $attempt of $max_attempts..."
-            sleep "$((attempt * 2))"
-        fi
-        
-        if git clone "$repo_url" "$worktree_path" 2>/dev/null; then
-            clone_success=true
-        fi
-    done
-    
-    if [ "$clone_success" = false ]; then
-        echo "Error: Failed to clone repository after $max_attempts attempts" >&2
+    git clone "$repo_url" "$worktree_path" 2>/dev/null || {
+        echo "Error: Failed to clone repository" >&2
         exit 1
-    fi
+    }
     
     echo "Creating branch '$branch_name'..."
-    if git -C "$worktree_path" checkout -b "$branch_name" origin/main 2>/dev/null; then
-        :
-    elif git -C "$worktree_path" checkout -b "$branch_name" main 2>/dev/null; then
-        :
-    else
+    (cd "$worktree_path" && git checkout -b "$branch_name" origin/main 2>/dev/null || git checkout -b "$branch_name" main 2>/dev/null) || {
         echo "Warning: Could not checkout branch (may need to run from within worktree after session)" >&2
-    fi
+    }
     
     echo "Worktree created at: $worktree_path"
 }
@@ -167,17 +145,15 @@ check_pr_status() {
         token="${GITEA_TOKEN:-}"
     fi
     
-    local response_file="$KUGETSU_DIR/.pr_status_response_$$.json"
+    local response
     if [ -n "$token" ]; then
-        curl -s -H "Authorization: token $token" "$api_url" > "$response_file" 2>/dev/null || printf '{}' > "$response_file"
+        response=$(curl -s -H "Authorization: token $token" "$api_url" 2>/dev/null || echo "{}")
     else
-        curl -s "$api_url" > "$response_file" 2>/dev/null || printf '{}' > "$response_file"
+        response=$(curl -s "$api_url" 2>/dev/null || echo "{}")
     fi
     
-    local state=$(python3 -c "import json; print(json.load(open('$response_file')).get('state', 'unknown'))" 2>/dev/null || echo "unknown")
-    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 "$response_file"
+    local state=$(echo "$response" | python3 -c "import json, sys; d=json.load(sys.stdin); print(d.get('state', 'unknown'))" 2>/dev/null || echo "unknown")
+    local merged=$(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")
     
     if [ "$merged" = "true" ]; then
         echo "merged"