prizmkit 1.1.91 → 1.1.93

package/bundled/VERSION.json

@@ -1,5 +1,5 @@
 {
-  "frameworkVersion": "1.1.91",
-  "bundledAt": "2026-07-01T17:51:47.362Z",
-  "bundledFrom": "5dcb047"
+  "frameworkVersion": "1.1.93",
+  "bundledAt": "2026-07-02T17:03:22.377Z",
+  "bundledFrom": "dc86f56"
 }

package/bundled/dev-pipeline/.env.example

@@ -23,7 +23,6 @@
 
 # ─── Pipeline Execution ──────────────────────────────────────────────
 # MAX_RETRIES=3              # Max retry attempts per task before marking failed
-# SESSION_TIMEOUT=0          # Session timeout in seconds (0 = no limit)
 # VERBOSE=1                  # Verbose logging (1=on, 0=off)
 
 # ─── Feature Pipeline Only ────────────────────────────────────────────
@@ -45,6 +44,3 @@
 # CODEX_WAIT_STALE_KILL_THRESHOLD=3600  # Longer no-log window while Codex waits on subagents
 # CODEX_SUBAGENT_TIMEOUT_SECONDS=3300   # Codex subagent max runtime; defaults to wait threshold - 300
 # CB_SUBAGENT_STALE_KILL_THRESHOLD=3600 # Longer no-log window while CodeBuddy sub-agents are running
-# LOG_CLEANUP_ENABLED=1      # Periodic log cleanup (1=on, 0=off)
-# LOG_RETENTION_DAYS=14      # Delete logs older than N days
-# LOG_MAX_TOTAL_MB=1024      # Keep total logs under N MB via oldest-first cleanup

package/bundled/dev-pipeline/README.md

@@ -53,7 +53,6 @@ Main entry point. Drives the full feature development pipeline.
 | Option | Description |
 |--------|-------------|
 | `--dry-run` | Generate bootstrap prompt only, don't spawn AI session |
-| `--timeout N` | Override `SESSION_TIMEOUT` for this run (seconds) |
 | `--resume-phase N` | Resume from specific phase number |
 | `--no-reset` | Don't reset feature artifacts before running |
 
@@ -71,9 +70,6 @@ Main entry point. Drives the full feature development pipeline.
 
 # Resume from Phase 6 (implementation)
 ./.prizmkit/dev-pipeline/run-feature.sh run .prizmkit/plans/feature-list.json --resume-phase 6
-
-# With timeout per session
-SESSION_TIMEOUT=7200 ./.prizmkit/dev-pipeline/run-feature.sh run .prizmkit/plans/feature-list.json
 ```
 
 If `.prizmkit/plans/feature-list.json` path is omitted, defaults to `.prizmkit/plans/feature-list.json` in the project root.
@@ -140,7 +136,7 @@ Manages `run-feature.sh` as a background daemon process with PID tracking and lo
 ```bash
 ./.prizmkit/dev-pipeline/launch-feature-daemon.sh start .prizmkit/plans/feature-list.json \
   --mode standard \
-  --env "MAX_RETRIES=5 SESSION_TIMEOUT=3600 MODEL=claude-sonnet-4.6"
+  --env "MAX_RETRIES=5 MODEL=claude-sonnet-4.6"
 ```
 
 **Output (JSON on stdout for programmatic consumption):**
@@ -177,7 +173,7 @@ Equivalent to `run-feature.sh` but for the bug-fix pipeline.
 ./run-bugfix.sh help
 ```
 
-**Single-bug options:** `--dry-run`, `--timeout N` (same as `run-feature.sh`)
+**Single-bug options:** `--dry-run` (same as `run-feature.sh`)
 
 Processes bugs by: **severity** (critical > high > medium > low) then **priority** (high > medium > low).
 
@@ -342,7 +338,7 @@ python3 scripts/update-feature-status.py \
 | `complete` | `--feature-id` | Shortcut for manually marking completed |
 
 **Session status values (for `--session-status`):**
-`success`, `partial_resumable`, `partial_not_resumable`, `failed`, `crashed`, `timed_out`, `commit_missing`, `docs_missing`, `merge_conflict`
+`success`, `partial_resumable`, `partial_not_resumable`, `failed`, `crashed`, `commit_missing`, `docs_missing`, `merge_conflict`
 
 **Output (JSON to stdout):**
 
@@ -429,26 +425,6 @@ python3 scripts/detect-stuck.py \
 
 ---
 
-### `scripts/cleanup-logs.py` — Log File Cleanup
-
-Manages log file size by age and total size thresholds.
-
-```bash
-python3 scripts/cleanup-logs.py \
-  --state-dir <path> \
-  [--retention-days <n>] \
-  [--max-total-mb <n>] \
-  [--dry-run]
-```
-
-| Option | Default | Description |
-|--------|---------|-------------|
-| `--retention-days` | 14 | Delete files older than N days |
-| `--max-total-mb` | 1024 | If total > N MB, remove oldest first |
-| `--dry-run` | false | Show what would be deleted without deleting |
-
----
-
 ### `scripts/parse-stream-progress.py` — Real-Time Progress Parser
 
 Reads AI CLI `stream-json` output and extracts progress metrics.
@@ -533,7 +509,6 @@ Also exports: `log_info`, `log_warn`, `log_error`, `log_success` (with timestamp
 | Variable | Default | Used By | Description |
 |----------|---------|---------|-------------|
 | `MAX_RETRIES` | `3` | run-feature.sh | Max retry attempts per feature before marking as failed |
-| `SESSION_TIMEOUT` | `0` (none) | run-feature.sh, run-bugfix.sh | Timeout in seconds per AI CLI session. 0 = no timeout |
 | `PIPELINE_MODE` | (auto) | run-feature.sh, launch-feature-daemon.sh | Override mode for all features: `lite\|standard\|full` |
 | `ENABLE_CRITIC` | `false` | run-feature.sh, launch-feature-daemon.sh | Enable adversarial critic review: `true\|false` |
 | `DEV_BRANCH` | auto-generated | run-feature.sh | Custom git branch name (default: `dev/{feature-id}-{timestamp}`) |
@@ -555,21 +530,18 @@ Also exports: `log_info`, `log_warn`, `log_error`, `log_success` (with timestamp
 |----------|---------|---------|-------------|
 | `HEARTBEAT_INTERVAL` | `30` | run-feature.sh | Seconds between heartbeat log output |
 | `HEARTBEAT_STALE_THRESHOLD` | `600` | run-feature.sh | Seconds before a session is considered stale/stuck |
-| `LOG_CLEANUP_ENABLED` | `1` | run-feature.sh | Run log cleanup before pipeline execution |
-| `LOG_RETENTION_DAYS` | `14` | run-feature.sh | Delete logs older than N days |
-| `LOG_MAX_TOTAL_MB` | `1024` | run-feature.sh | Keep total log size under N MB |
 
 **Examples:**
 
 ```bash
 # All env vars in one invocation
-MAX_RETRIES=5 SESSION_TIMEOUT=7200 MODEL=claude-sonnet-4.6 VERBOSE=1 \
+MAX_RETRIES=5 MODEL=claude-sonnet-4.6 VERBOSE=1 \
   ./.prizmkit/dev-pipeline/run-feature.sh run .prizmkit/plans/feature-list.json
 
 # Via daemon with --env
 ./.prizmkit/dev-pipeline/launch-feature-daemon.sh start .prizmkit/plans/feature-list.json \
   --mode standard \
-  --env "MAX_RETRIES=5 SESSION_TIMEOUT=3600 AUTO_PUSH=1"
+  --env "MAX_RETRIES=5 AUTO_PUSH=1"
 ```
 
 ---
@@ -721,11 +693,10 @@ Features are executed in dependency order via DAG:
 
 1. **Bootstrap prompt** generated from feature spec, context, and acceptance criteria
 2. AI CLI spawned as background process with optional `--model` flag
-3. **Timeout watchdog** runs in parallel if `SESSION_TIMEOUT > 0`
-4. **Heartbeat monitor** prints progress every `HEARTBEAT_INTERVAL` seconds
-5. **Progress parser** (if stream-json supported) extracts phase/tool metrics
-6. On completion, `session-status.json` determines success/failure
-7. Feature status updated; on failure, retry count increments
+3. **Heartbeat monitor** prints progress every `HEARTBEAT_INTERVAL` seconds
+4. **Progress parser** (if stream-json supported) extracts phase/tool metrics
+5. On completion, `session-status.json` determines success/failure
+6. Feature status updated; on failure, retry count increments
 
 ### Heartbeat Output
 
@@ -882,7 +853,6 @@ run-bugfix.sh main loop
 |   +-- update-feature-status.py     # Feature state machine (8 actions)
 |   +-- update-bug-status.py         # Bug state machine (6 actions)
 |   +-- detect-stuck.py              # Detect stuck/stale features
-|   +-- cleanup-logs.py              # Age/size-based log cleanup
 |   +-- parse-stream-progress.py     # Real-time stream-json progress parser
 |
 +-- templates/

package/bundled/dev-pipeline/SCHEMA_ANALYSIS.md

@@ -344,7 +344,6 @@ pending, in_progress, completed, failed, skipped
 | `AI_CLI` | string | auto-detect | claude or cbc |
 | `MODEL` | string | (unset) | AI model override (per-task overrides this) |
 | `MAX_RETRIES` | integer | (not specified) | Retry attempts per task |
-| `SESSION_TIMEOUT` | integer | 0 | 0 = no limit |
 | `VERBOSE` | integer | (not specified) | 1=on, 0=off |
 | `ENABLE_CRITIC` | boolean | false | Adversarial review enable |
 | `PIPELINE_MODE` | string | auto-detect | lite/standard/full override |
@@ -356,9 +355,6 @@ pending, in_progress, completed, failed, skipped
 | `STALE_KILL_THRESHOLD` | integer | 900 | Auto-kill after N seconds without parent log progress |
 | `CODEX_WAIT_STALE_KILL_THRESHOLD` | integer | 3600 | Longer no-log stale window while Codex waits on subagents |
 | `CODEX_SUBAGENT_TIMEOUT_SECONDS` | integer | 3300 | Codex subagent max runtime |
-| `LOG_CLEANUP_ENABLED` | integer | 1 | Periodic cleanup |
-| `LOG_RETENTION_DAYS` | integer | 14 | Delete logs older than N days |
-| `LOG_MAX_TOTAL_MB` | integer | 1024 | Max total logs (MB) |
 
 **Priority:** Command-line env vars > .env file > defaults
 

package/bundled/dev-pipeline/assets/prizm-dev-team-integration.md

@@ -51,7 +51,6 @@ Located at `.prizmkit/dev-pipeline/scripts/`:
 | `check-session-status.py` | Read and validate session-status.json output |
 | `detect-stuck.py` | Detect stuck/hung pipeline sessions via heartbeat |
 | `parse-stream-progress.py` | Parse AI CLI output stream for progress tracking |
-| `cleanup-logs.py` | Clean up old pipeline logs and state files |
 | `utils.py` | Shared utility functions for pipeline scripts |
 
 ## Artifact Mapping
@@ -125,7 +124,6 @@ The agent MUST write `session-status.json` before exiting:
 | `status: "partial"`, `can_resume: false` | Retry from scratch |
 | `status: "failed"` | Retry (up to MAX_RETRIES) |
 | No status file (crash) | Treat as failed, retry |
-| Timeout (exit 124) | Treat as timed_out, retry |
 
 ## Team Naming Convention
 

package/bundled/dev-pipeline/launch-bugfix-daemon.sh

@@ -482,7 +482,6 @@ Examples:
 
 Environment Variables (pass via --env):
   MAX_RETRIES           Max retries per bug (default: 3)
-  SESSION_TIMEOUT       Session timeout in seconds (default: 0 = no limit)
   VERBOSE               Set to 1 for verbose AI CLI output
   HEARTBEAT_INTERVAL    Heartbeat log interval in seconds (default: 30)
   DEV_BRANCH            Custom dev branch name (default: auto-generated)

package/bundled/dev-pipeline/launch-feature-daemon.sh

@@ -106,7 +106,7 @@ cmd_start() {
             --env)
                 shift
                 if [[ $# -eq 0 ]]; then
-                    log_error "--env requires a value (e.g. --env \"MAX_RETRIES=5 SESSION_TIMEOUT=3600\")"
+                    log_error "--env requires a value (e.g. --env \"MAX_RETRIES=5\")"
                     exit 1
                 fi
                 env_overrides="$1"
@@ -609,7 +609,7 @@ Examples:
   ./launch-feature-daemon.sh start --features F-001,F-003,F-007  # Run specific features
   ./launch-feature-daemon.sh start --mode full              # Full mode for complex features
   ./launch-feature-daemon.sh start --critic                  # Enable adversarial critic review
-  ./launch-feature-daemon.sh start --env "MAX_RETRIES=5 SESSION_TIMEOUT=7200"
+  ./launch-feature-daemon.sh start --env "MAX_RETRIES=5"
   ./launch-feature-daemon.sh start .prizmkit/plans/feature-list.json --mode full --critic --env "VERBOSE=1"
   ./launch-feature-daemon.sh status                       # Check if running (JSON on stdout)
   ./launch-feature-daemon.sh logs --follow                # Live log tailing
@@ -619,7 +619,6 @@ Examples:
 
 Environment Variables (pass via --env):
   MAX_RETRIES           Max retries per feature (default: 3)
-  SESSION_TIMEOUT       Session timeout in seconds (default: 0 = no limit)
   VERBOSE               Set to 1 for verbose AI CLI output
   HEARTBEAT_INTERVAL    Heartbeat log interval in seconds (default: 30)
   DEV_BRANCH            Custom dev branch name (default: auto-generated)

package/bundled/dev-pipeline/launch-refactor-daemon.sh

@@ -483,7 +483,6 @@ Examples:
 
 Environment Variables (pass via --env):
   MAX_RETRIES              Max retries per refactor (default: 3)
-  SESSION_TIMEOUT          Session timeout in seconds (default: 0 = no limit)
   VERBOSE                  Set to 1 for verbose AI CLI output
   STRICT_BEHAVIOR_CHECK    Force full test suite after each refactor (default: 1)
   HEARTBEAT_INTERVAL       Heartbeat log interval in seconds (default: 30)

package/bundled/dev-pipeline/lib/branch.sh

@@ -211,18 +211,21 @@ branch_save_wip() {
         return 0
     fi
 
-    # Check if there are any uncommitted changes (tracked or untracked, excluding gitignored)
+    # Check if there are any uncommitted changes (tracked or untracked,
+    # excluding gitignored and root-level hidden tool temporary worktrees)
     local has_changes
-    has_changes=$(git -C "$project_root" status --porcelain 2>/dev/null || true)
+    has_changes=$(prizm_git_status_safe "$project_root" || true)
     if [[ -z "$has_changes" ]]; then
         return 0
     fi
 
     log_warn "Saving uncommitted work-in-progress on branch: $dev_branch"
 
-    # Stage all changes (tracked + untracked, respects .gitignore)
-    if ! git -C "$project_root" add -A 2>/dev/null; then
-        log_warn "git add -A failed — uncommitted work may be lost on branch switch"
+    # Stage all changes (tracked + untracked, respects .gitignore), excluding
+    # root-level hidden tool temporary worktrees so nested agent repos are not
+    # recorded as accidental gitlinks in the user's project.
+    if ! prizm_git_add_all_safe "$project_root"; then
+        log_warn "git add failed — uncommitted work may be lost on branch switch"
         return 0
     fi
 

package/bundled/dev-pipeline/lib/common.sh

@@ -23,6 +23,128 @@ log_warn()    { echo -e "${YELLOW}[WARN]${NC}    $(date '+%Y-%m-%d %H:%M:%S') $*
 log_error()   { echo -e "${RED}[ERROR]${NC}   $(date '+%Y-%m-%d %H:%M:%S') $*"; }
 log_success() { echo -e "${GREEN}[SUCCESS]${NC} $(date '+%Y-%m-%d %H:%M:%S') $*"; }
 
+prizm_require_positive_int() {
+    local option_name="$1"
+    local option_value="$2"
+    if [[ ! "$option_value" =~ ^[1-9][0-9]*$ ]]; then
+        log_error "$option_name must be a positive integer: $option_value"
+        exit 1
+    fi
+}
+
+# Ignore temporary git worktrees created under root-level hidden AI tool dirs
+# matching .<tool>/worktree(s), without hiding normal source directories.
+PRIZM_GIT_HIDDEN_TOOL_WORKTREE_EXCLUDES=(
+    ':(top,exclude,glob).*/worktree'
+    ':(top,exclude,glob).*/worktree/**'
+    ':(top,exclude,glob).*/worktrees'
+    ':(top,exclude,glob).*/worktrees/**'
+)
+
+prizm_git_status_safe() {
+    local project_root="$1"
+    git -C "$project_root" status --porcelain -- . \
+        "${PRIZM_GIT_HIDDEN_TOOL_WORKTREE_EXCLUDES[@]}" 2>/dev/null
+}
+
+prizm_git_add_all_safe() {
+    local project_root="$1"
+    git -C "$project_root" add -A -- . \
+        "${PRIZM_GIT_HIDDEN_TOOL_WORKTREE_EXCLUDES[@]}" 2>/dev/null
+}
+
+prizm_git_relative_path() {
+    local project_root="$1"
+    local target_path="$2"
+    python3 - "$project_root" "$target_path" <<'PY' 2>/dev/null || true
+import os
+import sys
+root = os.path.abspath(sys.argv[1])
+target = os.path.abspath(sys.argv[2])
+print(os.path.relpath(target, root).replace(os.sep, "/"))
+PY
+}
+
+prizm_git_status_non_bookkeeping() {
+    local project_root="$1"
+    local state_dir="$2"
+    local list_path="$3"
+
+    local state_rel list_rel
+    state_rel="$(prizm_git_relative_path "$project_root" "$state_dir")"
+    list_rel="$(prizm_git_relative_path "$project_root" "$list_path")"
+
+    local line path
+    while IFS= read -r line; do
+        [[ -n "$line" ]] || continue
+        path="${line:3}"
+        if [[ "$path" == *" -> "* ]]; then
+            path="${path##* -> }"
+        fi
+        path="${path%\"}"
+        path="${path#\"}"
+        path="${path#./}"
+        if [[ -n "$list_rel" && "$path" == "$list_rel" ]]; then
+            continue
+        fi
+        if [[ -n "$state_rel" && ( "$path" == "$state_rel" || "$path" == "$state_rel/"* ) ]]; then
+            continue
+        fi
+        printf '%s\n' "$line"
+    done < <(prizm_git_status_safe "$project_root")
+}
+
+prizm_git_status_bookkeeping() {
+    local project_root="$1"
+    local state_dir="$2"
+    local list_path="$3"
+
+    local state_rel list_rel
+    state_rel="$(prizm_git_relative_path "$project_root" "$state_dir")"
+    list_rel="$(prizm_git_relative_path "$project_root" "$list_path")"
+
+    local line path
+    while IFS= read -r line; do
+        [[ -n "$line" ]] || continue
+        path="${line:3}"
+        if [[ "$path" == *" -> "* ]]; then
+            path="${path##* -> }"
+        fi
+        path="${path%\"}"
+        path="${path#\"}"
+        path="${path#./}"
+        if [[ -n "$list_rel" && "$path" == "$list_rel" ]]; then
+            printf '%s\n' "$line"
+            continue
+        fi
+        if [[ -n "$state_rel" && ( "$path" == "$state_rel" || "$path" == "$state_rel/"* ) ]]; then
+            printf '%s\n' "$line"
+        fi
+    done < <(prizm_git_status_safe "$project_root")
+}
+
+prizm_git_commit_paths() {
+    local project_root="$1"
+    local message="$2"
+    shift 2
+
+    local paths=()
+    local path rel_path
+    for path in "$@"; do
+        [[ -n "$path" && -e "$path" ]] || continue
+        rel_path="$(prizm_git_relative_path "$project_root" "$path")"
+        [[ -n "$rel_path" ]] || continue
+        paths+=("$rel_path")
+    done
+    [[ ${#paths[@]} -gt 0 ]] || return 0
+
+    git -C "$project_root" add -- "${paths[@]}" 2>/dev/null || true
+    if ! git -C "$project_root" diff --cached --quiet -- "${paths[@]}" 2>/dev/null; then
+        git -C "$project_root" commit --no-verify -m "$message" -- "${paths[@]}" 2>/dev/null || true
+    fi
+}
+
+
 # ============================================================
 # Path resolution (single source of truth)
 # ============================================================

package/bundled/dev-pipeline/lib/heartbeat.sh

@@ -46,6 +46,7 @@ start_heartbeat() {
         local prev_progress_signature=""
         local prev_error_loop_signature=""
         local stale_seconds=0
+        local stale_reason="stale_session"
         while kill -0 "$cli_pid" 2>/dev/null; do
             sleep "$heartbeat_interval"
             elapsed=$((elapsed + heartbeat_interval))
@@ -240,16 +241,20 @@ PY
             # child activity as the primary progress signals — the parent process is
             # still running and children may still be producing output.
             if [[ "$error_loop_detected" == "true" ]]; then
+                stale_reason="error_loop"
                 stale_seconds=$effective_stale_kill_threshold
             elif [[ "$log_truncated" == "true" ]]; then
+                stale_reason="stale_session"
                 if [[ $progress_advanced -gt 0 || $child_growth -gt 0 ]]; then
                     stale_seconds=0
                 else
                     stale_seconds=$((stale_seconds + heartbeat_interval))
                 fi
             elif [[ $growth -le 0 && $child_growth -eq 0 && $progress_advanced -eq 0 ]]; then
+                stale_reason="stale_session"
                 stale_seconds=$((stale_seconds + heartbeat_interval))
             else
+                stale_reason="stale_session"
                 stale_seconds=0
             fi
 
@@ -333,14 +338,19 @@ PY
             # stale window to surface stuck agents promptly.
             if [[ $effective_stale_kill_threshold -gt 0 && $stale_seconds -ge $effective_stale_kill_threshold ]]; then
                 local stale_mins=$((stale_seconds / 60))
-                echo -e "  ${RED}[HEARTBEAT]${NC} ${mins}m${secs}s | log: ${size_display} | ${RED}STALE-KILL: no progress for ${stale_mins}m (threshold: ${effective_stale_kill_threshold}s)${NC}"
-                echo -e "  ${RED}[HEARTBEAT]${NC} Killing AI CLI process $cli_pid (stale session)..."
+                if [[ "$stale_reason" == "error_loop" ]]; then
+                    echo -e "  ${RED}[HEARTBEAT]${NC} ${mins}m${secs}s | log: ${size_display} | ${RED}STALE-KILL: repeated read-offset/wasted-call error loop (threshold: ${effective_stale_kill_threshold}s)${NC}"
+                    echo -e "  ${RED}[HEARTBEAT]${NC} Killing AI CLI process $cli_pid (error loop)..."
+                else
+                    echo -e "  ${RED}[HEARTBEAT]${NC} ${mins}m${secs}s | log: ${size_display} | ${RED}STALE-KILL: no progress for ${stale_mins}m (threshold: ${effective_stale_kill_threshold}s)${NC}"
+                    echo -e "  ${RED}[HEARTBEAT]${NC} Killing AI CLI process $cli_pid (stale session)..."
+                fi
                 # Write the marker before killing. Some CLIs exit quickly, and the
                 # parent runner may stop this heartbeat process immediately after
                 # wait(1) returns.
                 local _marker_dir
                 _marker_dir="$(dirname "$session_log")"
-                echo "{\"killed_at\": \"$(date -u +%Y-%m-%dT%H:%M:%SZ)\", \"reason\": \"stale_session\", \"stale_seconds\": $stale_seconds, \"threshold\": $effective_stale_kill_threshold}" > "$_marker_dir/stale-kill.json" 2>/dev/null || true
+                echo "{\"killed_at\": \"$(date -u +%Y-%m-%dT%H:%M:%SZ)\", \"reason\": \"${stale_reason}\", \"stale_seconds\": $stale_seconds, \"threshold\": $effective_stale_kill_threshold}" > "$_marker_dir/stale-kill.json" 2>/dev/null || true
                 kill -TERM "$cli_pid" 2>/dev/null || true
                 # Give process 10s to exit gracefully, then force kill
                 local stale_kill_grace_seconds="${STALE_KILL_GRACE_SECONDS:-10}"