prizmkit 1.1.6 → 1.1.8

package/bundled/dev-pipeline/run-bugfix.sh

@@ -5,12 +5,12 @@ set -euo pipefail
 # dev-pipeline/run-bugfix.sh - Autonomous Bug Fix Pipeline Runner
 #
 # Drives the prizm-dev-team through iterative AI CLI sessions to
-# fix bugs from a bug-fix-list.json specification.
+# fix bugs from a .prizmkit/plans/bug-fix-list.json specification.
 #
 # Usage:
-#   ./run-bugfix.sh run [bug-fix-list.json]          Run all bugs
+#   ./run-bugfix.sh run [.prizmkit/plans/bug-fix-list.json]          Run all bugs
 #   ./run-bugfix.sh run <bug-id> [options]            Run a single bug
-#   ./run-bugfix.sh status [bug-fix-list.json]        Show pipeline status
+#   ./run-bugfix.sh status [.prizmkit/plans/bug-fix-list.json]        Show pipeline status
 #   ./run-bugfix.sh reset                             Clear all state
 #
 # Environment Variables:
@@ -30,7 +30,8 @@ set -euo pipefail
 # ============================================================
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-STATE_DIR="$SCRIPT_DIR/bugfix-state"
+PROJECT_ROOT="$(dirname "$SCRIPT_DIR")"
+STATE_DIR="${PROJECT_ROOT}/.prizmkit/state/bugfix"
 SCRIPTS_DIR="$SCRIPT_DIR/scripts"
 
 # Configuration
@@ -272,7 +273,7 @@ sys.exit(0)
         --max-retries "$max_retries" \
         --action update >/dev/null 2>&1 || true
 
-    # Commit bug-fix-list.json status update (pipeline management commit)
+    # Commit .prizmkit/plans/bug-fix-list.json status update (pipeline management commit)
     if ! git -C "$project_root" diff --quiet "$bug_list" 2>/dev/null; then
         git -C "$project_root" add "$bug_list"
         git -C "$project_root" commit --no-verify -m "chore($bug_id): update bug status" 2>/dev/null || true
@@ -352,10 +353,14 @@ run_one() {
     local bug_id=""
     local bug_list=""
     local dry_run=false
+    local do_clean=false
+    local no_reset=false
 
     while [[ $# -gt 0 ]]; do
         case "$1" in
             --dry-run) dry_run=true; shift ;;
+            --clean) do_clean=true; shift ;;
+            --no-reset) no_reset=true; shift ;;
             --timeout) shift; SESSION_TIMEOUT="${1:-0}"; shift ;;
             B-*|b-*) bug_id="$1"; shift ;;
             *) bug_list="$1"; shift ;;
@@ -370,7 +375,7 @@ run_one() {
     fi
 
     if [[ -z "$bug_list" ]]; then
-        bug_list="bug-fix-list.json"
+        bug_list=".prizmkit/plans/bug-fix-list.json"
     fi
     if [[ ! "$bug_list" = /* ]]; then
         bug_list="$(pwd)/$bug_list"
@@ -399,7 +404,7 @@ run_one() {
         local _gitignore_path
         _gitignore_path="$(cd "$SCRIPT_DIR/.." && pwd)/.gitignore"
         local _state_rel
-        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo "dev-pipeline/bugfix-state")
+        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo ".prizmkit/state/bugfix")
         if [[ -f "$_gitignore_path" ]]; then
             if ! grep -qF "$_state_rel" "$_gitignore_path" 2>/dev/null; then
                 printf '\n# Pipeline runtime state (auto-added by dev-pipeline)\n%s/\n' "$_state_rel" >> "$_gitignore_path"
@@ -437,12 +442,48 @@ for bug in data.get('bugs', []):
 sys.exit(1)
 " "$bug_list" "$bug_id" 2>/dev/null) || bug_severity="medium"
 
-    # Reset bug status
-    python3 "$SCRIPTS_DIR/update-bug-status.py" \
-        --bug-list "$bug_list" \
-        --state-dir "$STATE_DIR" \
-        --bug-id "$bug_id" \
-        --action reset >/dev/null 2>&1 || true
+    # Optional Clean
+    if [[ "$do_clean" == true ]]; then
+        if [[ "$dry_run" == true ]]; then
+            log_warn "Dry-run mode: --clean ignored (no artifacts will be deleted)"
+        else
+            log_info "Cleaning artifacts for $bug_id..."
+
+            local project_root
+            project_root="$(cd "$SCRIPT_DIR/.." && pwd)"
+
+            local bugfix_dir="$project_root/.prizmkit/bugfix/$bug_id"
+            if [[ -d "$bugfix_dir" ]]; then
+                rm -rf "$bugfix_dir"
+                log_info "Removed $bugfix_dir"
+            fi
+
+            local dev_team_dir="$project_root/.dev-team"
+            if [[ -d "$dev_team_dir" ]]; then
+                rm -rf "$dev_team_dir"
+                log_info "Removed $dev_team_dir"
+            fi
+
+            local bug_state_dir="$STATE_DIR/bugs/$bug_id"
+            if [[ -d "$bug_state_dir" ]]; then
+                rm -rf "$bug_state_dir"
+                log_info "Removed $bug_state_dir"
+            fi
+        fi
+    fi
+
+    # Reset bug status (conditional)
+    if [[ "$no_reset" == false && "$dry_run" == false ]]; then
+        python3 "$SCRIPTS_DIR/update-bug-status.py" \
+            --bug-list "$bug_list" \
+            --state-dir "$STATE_DIR" \
+            --bug-id "$bug_id" \
+            --action reset >/dev/null 2>&1 || {
+            log_warn "Failed to reset bug status (may already be pending)"
+        }
+    elif [[ "$dry_run" == true && "$no_reset" == false ]]; then
+        log_info "Dry-run mode: skipping status reset"
+    fi
 
     # Generate bootstrap prompt
     local run_id session_id session_dir bootstrap_prompt
@@ -551,7 +592,7 @@ sys.exit(1)
 # ============================================================
 
 main() {
-    local bug_list="${1:-bug-fix-list.json}"
+    local bug_list="${1:-.prizmkit/plans/bug-fix-list.json}"
 
     if [[ ! "$bug_list" = /* ]]; then
         bug_list="$(pwd)/$bug_list"
@@ -561,7 +602,7 @@ main() {
     if [[ ! -f "$bug_list" ]]; then
         log_error "Bug fix list not found: $bug_list"
         log_info "Create a bug fix list first using the bug-planner skill,"
-        log_info "or provide a path: ./run-bugfix.sh run <path-to-bug-fix-list.json>"
+        log_info "or provide a path: ./run-bugfix.sh run <path-to-.prizmkit/plans/bug-fix-list.json>"
         exit 1
     fi
 
@@ -593,7 +634,7 @@ main() {
         local _gitignore_path
         _gitignore_path="$(cd "$SCRIPT_DIR/.." && pwd)/.gitignore"
         local _state_rel
-        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo "dev-pipeline/bugfix-state")
+        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo ".prizmkit/state/bugfix")
         if [[ -f "$_gitignore_path" ]]; then
             if ! grep -qF "$_state_rel" "$_gitignore_path" 2>/dev/null; then
                 printf '\n# Pipeline runtime state (auto-added by dev-pipeline)\n%s/\n' "$_state_rel" >> "$_gitignore_path"
@@ -647,11 +688,14 @@ main() {
     while true; do
         # Find next bug to process
         local next_bug
-        next_bug=$(python3 "$SCRIPTS_DIR/update-bug-status.py" \
+        if ! next_bug=$(python3 "$SCRIPTS_DIR/update-bug-status.py" \
             --bug-list "$bug_list" \
             --state-dir "$STATE_DIR" \
             --max-retries "$MAX_RETRIES" \
-            --action get_next 2>/dev/null) || true
+            --action get_next 2>/dev/null); then
+            log_error "Failed to get next bug"
+            break
+        fi
 
         if [[ "$next_bug" == "PIPELINE_COMPLETE" ]]; then
             echo ""
@@ -745,14 +789,16 @@ show_help() {
     echo "Usage: $0 <command> [options]"
     echo ""
     echo "Commands:"
-    echo "  run [bug-fix-list.json]                 Run all bugs by severity/priority order"
+    echo "  run [.prizmkit/plans/bug-fix-list.json]                 Run all bugs by severity/priority order"
     echo "  run <bug-id> [options]                   Run a single bug fix"
-    echo "  status [bug-fix-list.json]               Show bug fix pipeline status"
+    echo "  status [.prizmkit/plans/bug-fix-list.json]               Show bug fix pipeline status"
     echo "  reset                                    Clear all bugfix state"
     echo "  help                                     Show this help message"
     echo ""
     echo "Single Bug Options (run <bug-id>):"
     echo "  --dry-run                   Generate bootstrap prompt only, don't spawn session"
+    echo "  --clean                     Delete artifacts and reset before running"
+    echo "  --no-reset                  Skip status reset (preserve retry count)"
     echo "  --timeout N                 Session timeout in seconds (default: 0 = no limit)"
     echo ""
     echo "Environment Variables:"
@@ -767,8 +813,10 @@ show_help() {
     echo ""
     echo "Examples:"
     echo "  ./run-bugfix.sh run                                    # Run all bugs"
-    echo "  ./run-bugfix.sh run bug-fix-list.json                  # Custom bug list"
+    echo "  ./run-bugfix.sh run .prizmkit/plans/bug-fix-list.json                  # Custom bug list"
     echo "  ./run-bugfix.sh run B-001 --dry-run                    # Inspect generated prompt"
+    echo "  ./run-bugfix.sh run B-001 --clean                      # Clean artifacts + reset + run"
+    echo "  ./run-bugfix.sh run B-001 --no-reset                   # Retry without resetting status"
     echo "  ./run-bugfix.sh run B-001 --timeout 3600               # 1h timeout"
     echo "  ./run-bugfix.sh status                                 # Show status"
     echo "  MAX_RETRIES=5 ./run-bugfix.sh run                      # Custom retries"
@@ -780,7 +828,7 @@ case "${1:-run}" in
         if [[ "${1:-}" =~ ^[Bb]-[0-9]+ ]]; then
             run_one "$@"
         else
-            main "${1:-bug-fix-list.json}"
+            main "${1:-.prizmkit/plans/bug-fix-list.json}"
         fi
         ;;
     status)
@@ -790,7 +838,7 @@ case "${1:-run}" in
             exit 1
         fi
         python3 "$SCRIPTS_DIR/update-bug-status.py" \
-            --bug-list "${2:-bug-fix-list.json}" \
+            --bug-list "${2:-.prizmkit/plans/bug-fix-list.json}" \
             --state-dir "$STATE_DIR" \
             --action status
         ;;

package/bundled/dev-pipeline/run-feature.sh

@@ -9,9 +9,9 @@ set -euo pipefail
 # from a feature list.
 #
 # Usage:
-#   ./run-feature.sh run [feature-list.json]            Run all features
+#   ./run-feature.sh run [.prizmkit/plans/feature-list.json]            Run all features
 #   ./run-feature.sh run <feature-id> [options]         Run a single feature
-#   ./run-feature.sh status [feature-list.json]         Show pipeline status
+#   ./run-feature.sh status [.prizmkit/plans/feature-list.json]         Show pipeline status
 #   ./run-feature.sh reset                              Clear all state
 #
 # Environment Variables:
@@ -33,7 +33,8 @@ set -euo pipefail
 # ============================================================
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-STATE_DIR="$SCRIPT_DIR/state"
+PROJECT_ROOT="$(dirname "$SCRIPT_DIR")"
+STATE_DIR="${PROJECT_ROOT}/.prizmkit/state/features"
 SCRIPTS_DIR="$SCRIPT_DIR/scripts"
 
 # Configuration (override via environment variables)
@@ -345,7 +346,7 @@ sys.exit(0)
         --max-retries "$max_retries" \
         --action update 2>&1) || {
         log_error "Failed to update feature status: $update_output"
-        log_error "feature-list.json may be out of sync. Manual intervention needed."
+        log_error ".prizmkit/plans/feature-list.json may be out of sync. Manual intervention needed."
     }
 
     # Commit feature status update (pipeline management commit)
@@ -514,7 +515,7 @@ run_one() {
 
     # Default feature list
     if [[ -z "$feature_list" ]]; then
-        feature_list="feature-list.json"
+        feature_list=".prizmkit/plans/feature-list.json"
     fi
 
     # Resolve to absolute path
@@ -542,9 +543,12 @@ run_one() {
     if [[ ! -f "$STATE_DIR/pipeline.json" ]]; then
         log_info "Initializing pipeline state for single-feature run..."
         local init_result
-        init_result=$(python3 "$SCRIPTS_DIR/init-pipeline.py" \
+        if ! init_result=$(python3 "$SCRIPTS_DIR/init-pipeline.py" \
             --feature-list "$feature_list" \
-            --state-dir "$STATE_DIR" 2>&1)
+            --state-dir "$STATE_DIR" 2>&1); then
+            log_error "Pipeline initialization failed (script error)"
+            exit 1
+        fi
 
         local init_valid
         init_valid=$(echo "$init_result" | python3 -c "import sys,json; print(json.load(sys.stdin).get('valid', False))" 2>/dev/null || echo "False")
@@ -829,7 +833,7 @@ sys.exit(1)
 # ============================================================
 
 main() {
-    local feature_list="${1:-feature-list.json}"
+    local feature_list="${1:-.prizmkit/plans/feature-list.json}"
     local features_filter="${2:-}"
 
     # Resolve to absolute path
@@ -843,18 +847,18 @@ main() {
     if [[ ! -f "$feature_list" ]]; then
         log_error "Feature list not found: $feature_list"
         log_info "Create a feature list first using the feature-planner skill,"
-        log_info "or provide a path: ./run-feature.sh run <path-to-feature-list.json>"
+        log_info "or provide a path: ./run-feature.sh run <path-to-.prizmkit/plans/feature-list.json>"
         exit 1
     fi
 
-    # Validate feature-list.json is at project root
+    # Validate .prizmkit/plans/feature-list.json is at project root
     local fl_dir
     fl_dir="$(cd "$(dirname "$feature_list")" && pwd)"
     local project_root
     project_root="$(pwd)"
     if [[ "$fl_dir" != "$project_root" ]]; then
-        log_warn "feature-list.json is not at project root ($project_root), found at $fl_dir"
-        log_warn "Pipeline expects feature-list.json at project root. Proceeding but results may be unstable."
+        log_warn ".prizmkit/plans/feature-list.json is not at project root ($project_root), found at $fl_dir"
+        log_warn "Pipeline expects .prizmkit/plans/feature-list.json at project root. Proceeding but results may be unstable."
     fi
 
     check_dependencies
@@ -885,7 +889,7 @@ main() {
         local _gitignore_path
         _gitignore_path="$(cd "$SCRIPT_DIR/.." && pwd)/.gitignore"
         local _state_rel
-        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo "dev-pipeline/state")
+        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo ".prizmkit/state/features")
         if [[ -f "$_gitignore_path" ]]; then
             if ! grep -qF "$_state_rel" "$_gitignore_path" 2>/dev/null; then
                 printf '\n# Pipeline runtime state (auto-added by dev-pipeline)\n%s/\n' "$_state_rel" >> "$_gitignore_path"
@@ -965,8 +969,13 @@ for f in data.get('stuck_features', []):
         if [[ -n "$features_filter" ]]; then
             _get_next_args+=(--features "$features_filter")
         fi
-        next_feature=$(python3 "$SCRIPTS_DIR/update-feature-status.py" \
-            "${_get_next_args[@]}" 2>/dev/null) || true
+        if ! next_feature=$(python3 "$SCRIPTS_DIR/update-feature-status.py" \
+            "${_get_next_args[@]}" 2>/dev/null); then
+
+            log_error "Failed to get next feature"
+            break
+        fi
+
 
         if [[ "$next_feature" == "PIPELINE_COMPLETE" ]]; then
             echo ""
@@ -1150,10 +1159,10 @@ show_help() {
     echo "Usage: $0 <command> [options]"
     echo ""
     echo "Commands:"
-    echo "  run [feature-list.json] [--features <filter>]  Run features (all or filtered subset)"
+    echo "  run [.prizmkit/plans/feature-list.json] [--features <filter>]  Run features (all or filtered subset)"
     echo "  run <feature-id> [options]              Run a single feature"
-    echo "  status [feature-list.json]               Show pipeline status"
-    echo "  unskip [feature-id] [feature-list.json]  Reset auto-skipped/failed features"
+    echo "  status [.prizmkit/plans/feature-list.json]               Show pipeline status"
+    echo "  unskip [feature-id] [.prizmkit/plans/feature-list.json]  Reset auto-skipped/failed features"
     echo "  test-cli                                 Test AI CLI: show detected CLI, version, and model"
     echo "  reset                                    Clear all state and start fresh"
     echo "  help                                     Show this help message"
@@ -1209,7 +1218,7 @@ case "${1:-run}" in
             run_one "$@"
         else
             # Parse positional and --features flag
-             _run_feature_list="feature-list.json"
+             _run_feature_list=".prizmkit/plans/feature-list.json"
              _run_features_filter=""
             while [[ $# -gt 0 ]]; do
                 case "$1" in
@@ -1238,7 +1247,7 @@ case "${1:-run}" in
             exit 1
         fi
         python3 "$SCRIPTS_DIR/update-feature-status.py" \
-            --feature-list "${2:-feature-list.json}" \
+            --feature-list "${2:-.prizmkit/plans/feature-list.json}" \
             --state-dir "$STATE_DIR" \
             --action status
         ;;
@@ -1311,7 +1320,7 @@ case "${1:-run}" in
             log_error "No pipeline state found. Run './run-feature.sh run' first."
             exit 1
         fi
-        _unskip_feature_list="feature-list.json"
+        _unskip_feature_list=".prizmkit/plans/feature-list.json"
         _unskip_feature_id=""
         shift || true
         # Parse arguments: optional feature-id and feature-list path

package/bundled/dev-pipeline/run-refactor.sh

@@ -5,12 +5,12 @@ set -euo pipefail
 # dev-pipeline/run-refactor.sh - Autonomous Refactor Pipeline Runner
 #
 # Drives the prizm-dev-team through iterative AI CLI sessions to
-# execute refactors from a refactor-list.json specification.
+# execute refactors from a .prizmkit/plans/refactor-list.json specification.
 #
 # Usage:
-#   ./run-refactor.sh run [refactor-list.json]          Run all refactors
+#   ./run-refactor.sh run [.prizmkit/plans/refactor-list.json]          Run all refactors
 #   ./run-refactor.sh run <refactor-id> [options]       Run a single refactor
-#   ./run-refactor.sh status [refactor-list.json]       Show pipeline status
+#   ./run-refactor.sh status [.prizmkit/plans/refactor-list.json]       Show pipeline status
 #   ./run-refactor.sh reset                             Clear all state
 #
 # Environment Variables:
@@ -31,7 +31,8 @@ set -euo pipefail
 # ============================================================
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-STATE_DIR="$SCRIPT_DIR/refactor-state"
+PROJECT_ROOT="$(dirname "$SCRIPT_DIR")"
+STATE_DIR="${PROJECT_ROOT}/.prizmkit/state/refactor"
 SCRIPTS_DIR="$SCRIPT_DIR/scripts"
 
 # Configuration
@@ -239,7 +240,7 @@ spawn_and_wait_session() {
         --max-retries "$max_retries" \
         --action update >/dev/null 2>&1 || true
 
-    # Commit refactor-list.json status update (pipeline management commit)
+    # Commit .prizmkit/plans/refactor-list.json status update (pipeline management commit)
     if ! git -C "$project_root" diff --quiet "$refactor_list" 2>/dev/null; then
         git -C "$project_root" add "$refactor_list"
         git -C "$project_root" commit --no-verify -m "chore($refactor_id): update refactor status" 2>/dev/null || true
@@ -337,7 +338,7 @@ run_one() {
     fi
 
     if [[ -z "$refactor_list" ]]; then
-        refactor_list="refactor-list.json"
+        refactor_list=".prizmkit/plans/refactor-list.json"
     fi
     if [[ ! "$refactor_list" = /* ]]; then
         refactor_list="$(pwd)/$refactor_list"
@@ -366,7 +367,7 @@ run_one() {
         local _gitignore_path
         _gitignore_path="$(cd "$SCRIPT_DIR/.." && pwd)/.gitignore"
         local _state_rel
-        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo "dev-pipeline/refactor-state")
+        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo ".prizmkit/state/refactor")
         if [[ -f "$_gitignore_path" ]]; then
             if ! grep -qF "$_state_rel" "$_gitignore_path" 2>/dev/null; then
                 printf '\n# Pipeline runtime state (auto-added by dev-pipeline)\n%s/\n' "$_state_rel" >> "$_gitignore_path"
@@ -521,7 +522,7 @@ sys.exit(1)
 # ============================================================
 
 main() {
-    local refactor_list="${1:-refactor-list.json}"
+    local refactor_list="${1:-.prizmkit/plans/refactor-list.json}"
 
     if [[ ! "$refactor_list" = /* ]]; then
         refactor_list="$(pwd)/$refactor_list"
@@ -531,7 +532,7 @@ main() {
     if [[ ! -f "$refactor_list" ]]; then
         log_error "Refactor list not found: $refactor_list"
         log_info "Create a refactor list first using the refactor-planner skill,"
-        log_info "or provide a path: ./run-refactor.sh run <path-to-refactor-list.json>"
+        log_info "or provide a path: ./run-refactor.sh run <path-to-.prizmkit/plans/refactor-list.json>"
         exit 1
     fi
 
@@ -563,7 +564,7 @@ main() {
         local _gitignore_path
         _gitignore_path="$(cd "$SCRIPT_DIR/.." && pwd)/.gitignore"
         local _state_rel
-        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo "dev-pipeline/refactor-state")
+        _state_rel=$(python3 -c "import os; print(os.path.relpath('$STATE_DIR', '$(cd "$SCRIPT_DIR/.." && pwd)'))" 2>/dev/null || echo ".prizmkit/state/refactor")
         if [[ -f "$_gitignore_path" ]]; then
             if ! grep -qF "$_state_rel" "$_gitignore_path" 2>/dev/null; then
                 printf '\n# Pipeline runtime state (auto-added by dev-pipeline)\n%s/\n' "$_state_rel" >> "$_gitignore_path"
@@ -622,11 +623,14 @@ main() {
     while true; do
         # Find next refactor to process (dependency-topological order)
         local next_refactor
-        next_refactor=$(python3 "$SCRIPTS_DIR/update-refactor-status.py" \
+        if ! next_refactor=$(python3 "$SCRIPTS_DIR/update-refactor-status.py" \
             --refactor-list "$refactor_list" \
             --state-dir "$STATE_DIR" \
             --max-retries "$MAX_RETRIES" \
-            --action get_next 2>/dev/null) || true
+            --action get_next 2>/dev/null); then
+            log_error "Failed to get next refactor"
+            break
+        fi
 
         if [[ "$next_refactor" == "PIPELINE_COMPLETE" ]]; then
             echo ""
@@ -720,9 +724,9 @@ show_help() {
     echo "Usage: $0 <command> [options]"
     echo ""
     echo "Commands:"
-    echo "  run [refactor-list.json]                Run all refactors in dependency-topological order"
+    echo "  run [.prizmkit/plans/refactor-list.json]                Run all refactors in dependency-topological order"
     echo "  run <refactor-id> [options]              Run a single refactor"
-    echo "  status [refactor-list.json]              Show refactor pipeline status"
+    echo "  status [.prizmkit/plans/refactor-list.json]              Show refactor pipeline status"
     echo "  reset                                    Clear all refactor state"
     echo "  help                                     Show this help message"
     echo ""
@@ -743,7 +747,7 @@ show_help() {
     echo ""
     echo "Examples:"
     echo "  ./run-refactor.sh run                                    # Run all refactors"
-    echo "  ./run-refactor.sh run refactor-list.json                 # Custom refactor list"
+    echo "  ./run-refactor.sh run .prizmkit/plans/refactor-list.json                 # Custom refactor list"
     echo "  ./run-refactor.sh run R-001 --dry-run                    # Inspect generated prompt"
     echo "  ./run-refactor.sh run R-001 --timeout 3600               # 1h timeout"
     echo "  ./run-refactor.sh status                                 # Show status"
@@ -757,7 +761,7 @@ case "${1:-run}" in
         if [[ "${1:-}" =~ ^[Rr]-[0-9]+ ]]; then
             run_one "$@"
         else
-            main "${1:-refactor-list.json}"
+            main "${1:-.prizmkit/plans/refactor-list.json}"
         fi
         ;;
     status)
@@ -767,7 +771,7 @@ case "${1:-run}" in
             exit 1
         fi
         python3 "$SCRIPTS_DIR/update-refactor-status.py" \
-            --refactor-list "${2:-refactor-list.json}" \
+            --refactor-list "${2:-.prizmkit/plans/refactor-list.json}" \
             --state-dir "$STATE_DIR" \
             --action status
         ;;

package/bundled/dev-pipeline/scripts/cleanup-logs.py

@@ -9,8 +9,8 @@ Policies:
    until within threshold.
 
 Usage:
-  python3 cleanup-logs.py --state-dir dev-pipeline/state
-  python3 cleanup-logs.py --state-dir dev-pipeline/bugfix-state --retention-days 30 --max-total-mb 2048
+  python3 cleanup-logs.py --state-dir .prizmkit/state/features
+  python3 cleanup-logs.py --state-dir .prizmkit/state/bugfix --retention-days 30 --max-total-mb 2048
 """
 
 import argparse

package/bundled/dev-pipeline/scripts/detect-stuck.py

@@ -35,7 +35,7 @@ def parse_args():
     parser.add_argument(
         "--state-dir",
         required=True,
-        help="Path to the state/ directory",
+        help="Path to the state directory (default: .prizmkit/state/features)",
     )
     parser.add_argument(
         "--feature-id",
@@ -57,7 +57,7 @@ def parse_args():
     parser.add_argument(
         "--feature-list",
         default=None,
-        help="Path to feature-list.json (overrides pipeline.json reference)",
+        help="Path to .prizmkit/plans/feature-list.json (overrides pipeline.json reference)",
     )
     return parser.parse_args()
 
@@ -285,7 +285,7 @@ def check_dependency_deadlock(feature_id, feature_list_data, state_dir):
 
 
 def find_feature_list(state_dir):
-    """Attempt to locate and load feature-list.json via pipeline.json reference.
+    """Attempt to locate and load .prizmkit/plans/feature-list.json via pipeline.json reference.
 
     Resolves feature_list_path relative to state_dir when it is a relative path,
     so that pipeline.json is portable across machines and directory structures.

package/bundled/dev-pipeline/scripts/generate-bootstrap-prompt.py

@@ -38,13 +38,13 @@ def parse_args():
     parser = argparse.ArgumentParser(
         description=(
             "Generate a session-specific bootstrap prompt from a template "
-            "and feature-list.json."
+            "and .prizmkit/plans/feature-list.json."
         )
     )
     parser.add_argument(
         "--feature-list",
         required=True,
-        help="Path to feature-list.json",
+        help="Path to .prizmkit/plans/feature-list.json",
     )
     parser.add_argument(
         "--feature-id",
@@ -348,7 +348,7 @@ def get_prev_session_status(state_dir, feature_id):
 
 
 def _read_project_brief(project_root):
-    """Read project-brief.md from project root if it exists.
+    """Read project-brief.md from new or old location with fallback.
 
     Returns the file content as a string, or a fallback message if absent.
     This brief is generated by app-planner during interactive planning and
@@ -356,13 +356,25 @@ def _read_project_brief(project_root):
     marked [ ] for pending or [x] for completed. Feature sessions should mark
     items [x] and append key file paths when implementing relevant ideas.
     """
-    brief_path = os.path.join(project_root, "project-brief.md")
-    if os.path.isfile(brief_path):
-        try:
-            with open(brief_path, "r", encoding="utf-8") as f:
-                return f.read().strip()
-        except IOError:
-            return "(project-brief.md exists but could not be read)"
+    # Check both new and old paths for backward compatibility
+    new_path = os.path.join(project_root, ".prizmkit", "plans", "project-brief.md")
+    old_path = os.path.join(project_root, "project-brief.md")
+
+    for brief_path in [new_path, old_path]:
+        if os.path.isfile(brief_path):
+            try:
+                with open(brief_path, "r", encoding="utf-8") as f:
+                    content = f.read().strip()
+                    if brief_path == old_path:
+                        # Warn user about old path
+                        import sys
+                        print("⚠️  Migration notice: project-brief.md found in root. "
+                              "Please move to .prizmkit/plans/project-brief.md",
+                              file=sys.stderr)
+                    return content
+            except IOError:
+                return "(project-brief.md exists but could not be read)"
+
     return "(No project brief available)"
 
 
@@ -1179,12 +1191,12 @@ def build_replacements(args, feature, features, global_context, script_dir):
     validator_scripts_dir = os.path.join(project_root, "dev-pipeline", "scripts")
     init_script_path = os.path.join(validator_scripts_dir, "init-dev-team.py")
 
-    # Session status path (relative to dev-pipeline/)
+    # Session status path (relative to project root)
     session_status_path = os.path.join(
-        "dev-pipeline", "state", "features", args.feature_id,
+        ".prizmkit", "state", "features", args.feature_id,
         "sessions", args.session_id, "session-status.json",
     )
-    # Make it relative from project root
+    # Make it absolute from project root
     session_status_abs = os.path.join(project_root, session_status_path)
 
     prev_status = get_prev_session_status(args.state_dir, args.feature_id)
@@ -1221,7 +1233,7 @@ def build_replacements(args, feature, features, global_context, script_dir):
         critic_enabled = bool(feature.get("critic", False))
 
     # Determine critic count (from feature field, default 1)
-    # Multi-critic voting (3) must be explicitly set by the user in feature-list.json
+    # Multi-critic voting (3) must be explicitly set by the user in .prizmkit/plans/feature-list.json
     critic_count = feature.get("critic_count", 1)
 
     # Guard: if critic enabled but agent file missing, force disable and warn