prizmkit 1.1.97 → 1.1.99

package/bundled/VERSION.json

@@ -1,5 +1,5 @@
 {
-  "frameworkVersion": "1.1.97",
-  "bundledAt": "2026-07-03T07:22:35.206Z",
-  "bundledFrom": "732b89b"
+  "frameworkVersion": "1.1.99",
+  "bundledAt": "2026-07-04T12:56:36.867Z",
+  "bundledFrom": "54fe284"
 }

package/bundled/dev-pipeline/README.md

@@ -713,13 +713,13 @@ Features are executed in dependency order via DAG:
 
 ```bash
 # Live tail current session
-tail -f .prizmkit/state/features/features/F-*/sessions/*/logs/session.log
+tail -f .prizmkit/state/features/F-*/sessions/*/logs/session.log
 
 # Specific feature
-tail -f .prizmkit/state/features/features/F-003/sessions/*/logs/session.log
+tail -f .prizmkit/state/features/F-003/sessions/*/logs/session.log
 
 # Review completed session
-cat .prizmkit/state/features/features/F-003/sessions/F-003-*/logs/session.log | less
+cat .prizmkit/state/features/F-003/sessions/F-003-*/logs/session.log | less
 ```
 
 ### Pause & Resume
@@ -735,7 +735,7 @@ cat .prizmkit/state/features/features/F-003/sessions/F-003-*/logs/session.log |
 ./.prizmkit/dev-pipeline/run-feature.sh status .prizmkit/plans/feature-list.json
 
 # Review session logs
-cat .prizmkit/state/features/features/F-XXX/sessions/*/logs/session.log
+cat .prizmkit/state/features/F-XXX/sessions/*/logs/session.log
 
 # Option A: Fix manually and mark complete
 python3 .prizmkit/dev-pipeline/scripts/update-feature-status.py \
@@ -802,7 +802,7 @@ run-bugfix.sh main loop
 ```
 .prizmkit/state/bugfix/          # Runtime state (gitignored)
 +-- pipeline.json
-+-- bugs/B-XXX/
++-- B-XXX/
     +-- status.json
     +-- sessions/B-XXX-YYYYMMDDHHMMSS/
         +-- bootstrap-prompt.md

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

@@ -384,7 +384,7 @@ total = len(bugs)
 counts = {'completed': 0, 'in_progress': 0, 'failed': 0, 'pending': 0, 'needs_info': 0, 'skipped': 0}
 for bug in bugs:
     bid = bug.get('id', '')
-    sp = os.path.join('$STATE_DIR', 'bugs', bid, 'status.json')
+    sp = os.path.join('$STATE_DIR', bid, 'status.json')
     if os.path.isfile(sp):
         fs = json.load(open(sp))
         st = fs.get('status', 'pending')

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

@@ -487,7 +487,7 @@ total = len(features)
 counts = {'completed': 0, 'in_progress': 0, 'failed': 0, 'pending': 0, 'skipped': 0, 'auto_skipped': 0}
 for feat in features:
     fid = feat.get('id', '')
-    sp = os.path.join(state_dir, 'features', fid, 'status.json')
+    sp = os.path.join(state_dir, fid, 'status.json')
     if os.path.isfile(sp):
         fs = load_json(sp)
         st = fs.get('status', 'pending')

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

@@ -384,7 +384,7 @@ total = len(items)
 counts = {'completed': 0, 'in_progress': 0, 'failed': 0, 'pending': 0, 'skipped': 0, 'auto_skipped': 0}
 for item in items:
     rid = item.get('id', '')
-    sp = os.path.join('$STATE_DIR', 'refactors', rid, 'status.json')
+    sp = os.path.join('$STATE_DIR', rid, 'status.json')
     if os.path.isfile(sp):
         fs = json.load(open(sp))
         st = fs.get('status', 'pending')

package/bundled/dev-pipeline/reset-bug.sh

@@ -243,7 +243,7 @@ sys.exit(1)
     echo -e "${BOLD}  Reset: $CUR_BUG_ID — $BUG_TITLE${NC}"
     echo -e "${BOLD}════════════════════════════════════════════════════${NC}"
 
-    STATUS_FILE="$STATE_DIR/bugs/$CUR_BUG_ID/status.json"
+    STATUS_FILE="$STATE_DIR/$CUR_BUG_ID/status.json"
     # Read status from bug-fix-list.json (single source of truth)
     CURRENT_STATUS=$(python3 -c "
 import json, sys
@@ -270,7 +270,7 @@ print('?')
         log_info "PrizmKit artifacts: $BUGFIX_COUNT files in .prizmkit/bugfix/$CUR_BUG_ID/"
     fi
 
-    SESSIONS_DIR="$STATE_DIR/bugs/$CUR_BUG_ID/sessions"
+    SESSIONS_DIR="$STATE_DIR/$CUR_BUG_ID/sessions"
     SESSIONS_COUNT=0
     if [[ -d "$SESSIONS_DIR" ]]; then
         SESSIONS_COUNT=$(find "$SESSIONS_DIR" -mindepth 1 -maxdepth 1 -type d 2>/dev/null | wc -l | tr -d ' ')

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

@@ -252,7 +252,7 @@ sys.exit(1)
     echo -e "${BOLD}  Reset: $CUR_FEATURE_ID — $FEATURE_TITLE${NC}"
     echo -e "${BOLD}════════════════════════════════════════════════════${NC}"
 
-    STATUS_FILE="$STATE_DIR/features/$CUR_FEATURE_ID/status.json"
+    STATUS_FILE="$STATE_DIR/$CUR_FEATURE_ID/status.json"
     # Read status from feature-list.json (single source of truth)
     CURRENT_STATUS=$(python3 -c "
 import json, sys
@@ -279,7 +279,7 @@ print('?')
         log_info "PrizmKit artifacts: $SPECS_COUNT files in .prizmkit/specs/$FEATURE_SLUG/"
     fi
 
-    SESSIONS_DIR="$STATE_DIR/features/$CUR_FEATURE_ID/sessions"
+    SESSIONS_DIR="$STATE_DIR/$CUR_FEATURE_ID/sessions"
     SESSIONS_COUNT=0
     if [[ -d "$SESSIONS_DIR" ]]; then
         SESSIONS_COUNT=$(find "$SESSIONS_DIR" -mindepth 1 -maxdepth 1 -type d 2>/dev/null | wc -l | tr -d ' ')

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

@@ -241,7 +241,7 @@ sys.exit(1)
     echo -e "${BOLD}  Reset: $CUR_REFACTOR_ID — $REFACTOR_TITLE${NC}"
     echo -e "${BOLD}════════════════════════════════════════════════════${NC}"
 
-    STATUS_FILE="$STATE_DIR/refactors/$CUR_REFACTOR_ID/status.json"
+    STATUS_FILE="$STATE_DIR/$CUR_REFACTOR_ID/status.json"
     # Read status from refactor-list.json (single source of truth)
     CURRENT_STATUS=$(python3 -c "
 import json, sys
@@ -268,7 +268,7 @@ print('?')
         log_info "PrizmKit artifacts: $SPECS_COUNT files in .prizmkit/specs/$REFACTOR_SLUG/"
     fi
 
-    SESSIONS_DIR="$STATE_DIR/refactors/$CUR_REFACTOR_ID/sessions"
+    SESSIONS_DIR="$STATE_DIR/$CUR_REFACTOR_ID/sessions"
     SESSIONS_COUNT=0
     if [[ -d "$SESSIONS_DIR" ]]; then
         SESSIONS_COUNT=$(find "$SESSIONS_DIR" -mindepth 1 -maxdepth 1 -type d 2>/dev/null | wc -l | tr -d ' ')

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

@@ -519,7 +519,7 @@ sys.exit(1)
                 log_info "Removed $dev_team_dir"
             fi
 
-            local bug_state_dir="$STATE_DIR/bugs/$bug_id"
+            local bug_state_dir="$STATE_DIR/$bug_id"
             if [[ -d "$bug_state_dir" ]]; then
                 rm -rf "$bug_state_dir"
                 log_info "Removed $bug_state_dir"
@@ -544,7 +544,7 @@ sys.exit(1)
     local run_id session_id session_dir bootstrap_prompt
     run_id=$(jq -r '.run_id' "$STATE_DIR/pipeline.json")
     session_id="${bug_id}-$(date +%Y%m%d%H%M%S)"
-    session_dir="$STATE_DIR/bugs/$bug_id/sessions/$session_id"
+    session_dir="$STATE_DIR/$bug_id/sessions/$session_id"
     mkdir -p "$session_dir/logs"
 
     bootstrap_prompt="$session_dir/bootstrap-prompt.md"
@@ -553,7 +553,7 @@ sys.exit(1)
     local retry_count
     retry_count=$(python3 -c "
 import json, os
-status_path = os.path.join('$STATE_DIR', 'bugs', '$bug_id', 'status.json')
+status_path = os.path.join('$STATE_DIR', '$bug_id', 'status.json')
 if os.path.isfile(status_path):
     with open(status_path) as f:
         d = json.load(f)
@@ -564,7 +564,7 @@ else:
     local resume_phase
     resume_phase=$(python3 -c "
 import json, os
-status_path = os.path.join('$STATE_DIR', 'bugs', '$bug_id', 'status.json')
+status_path = os.path.join('$STATE_DIR', '$bug_id', 'status.json')
 if os.path.isfile(status_path):
     with open(status_path) as f:
         d = json.load(f)
@@ -1056,7 +1056,7 @@ DEPLOY_PROMPT_EOF
         run_id=$(jq -r '.run_id' "$STATE_DIR/pipeline.json")
         session_id="${bug_id}-$(date +%Y%m%d%H%M%S)"
 
-        local session_dir="$STATE_DIR/bugs/$bug_id/sessions/$session_id"
+        local session_dir="$STATE_DIR/$bug_id/sessions/$session_id"
         mkdir -p "$session_dir/logs"
 
         local bootstrap_prompt="$session_dir/bootstrap-prompt.md"

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

@@ -698,7 +698,7 @@ sys.exit(1)
                 log_info "Removed $dev_team_dir"
             fi
 
-            local feature_state_dir="$STATE_DIR/features/$feature_id"
+            local feature_state_dir="$STATE_DIR/$feature_id"
             if [[ -d "$feature_state_dir" ]]; then
                 rm -rf "$feature_state_dir"
                 log_info "Removed $feature_state_dir"
@@ -724,7 +724,7 @@ sys.exit(1)
     local run_id session_id session_dir bootstrap_prompt
     run_id=$(jq -r '.run_id' "$STATE_DIR/pipeline.json")
     session_id="${feature_id}-$(date +%Y%m%d%H%M%S)"
-    session_dir="$STATE_DIR/features/$feature_id/sessions/$session_id"
+    session_dir="$STATE_DIR/$feature_id/sessions/$session_id"
     mkdir -p "$session_dir/logs"
 
     bootstrap_prompt="$session_dir/bootstrap-prompt.md"
@@ -733,7 +733,7 @@ sys.exit(1)
     local retry_count
     retry_count=$(python3 -c "
 import json, os
-status_path = os.path.join('$STATE_DIR', 'features', '$feature_id', 'status.json')
+status_path = os.path.join('$STATE_DIR', '$feature_id', 'status.json')
 if os.path.isfile(status_path):
     with open(status_path) as f:
         d = json.load(f)
@@ -1275,7 +1275,7 @@ DEPLOY_PROMPT_EOF
         run_id=$(jq -r '.run_id' "$STATE_DIR/pipeline.json")
         session_id="${feature_id}-$(date +%Y%m%d%H%M%S)"
 
-        local session_dir="$STATE_DIR/features/$feature_id/sessions/$session_id"
+        local session_dir="$STATE_DIR/$feature_id/sessions/$session_id"
         mkdir -p "$session_dir/logs"
 
         local bootstrap_prompt="$session_dir/bootstrap-prompt.md"

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

@@ -544,7 +544,7 @@ sys.exit(1)
                 log_info "Removed $dev_team_dir"
             fi
 
-            local refactor_state_dir="$STATE_DIR/refactors/$refactor_id"
+            local refactor_state_dir="$STATE_DIR/$refactor_id"
             if [[ -d "$refactor_state_dir" ]]; then
                 rm -rf "$refactor_state_dir"
                 log_info "Removed $refactor_state_dir"
@@ -569,7 +569,7 @@ sys.exit(1)
     local run_id session_id session_dir bootstrap_prompt
     run_id=$(jq -r '.run_id' "$STATE_DIR/pipeline.json")
     session_id="${refactor_id}-$(date +%Y%m%d%H%M%S)"
-    session_dir="$STATE_DIR/refactors/$refactor_id/sessions/$session_id"
+    session_dir="$STATE_DIR/$refactor_id/sessions/$session_id"
     mkdir -p "$session_dir/logs"
 
     bootstrap_prompt="$session_dir/bootstrap-prompt.md"
@@ -578,7 +578,7 @@ sys.exit(1)
     local retry_count
     retry_count=$(python3 -c "
 import json, os
-status_path = os.path.join('$STATE_DIR', 'refactors', '$refactor_id', 'status.json')
+status_path = os.path.join('$STATE_DIR', '$refactor_id', 'status.json')
 if os.path.isfile(status_path):
     with open(status_path) as f:
         d = json.load(f)
@@ -589,7 +589,7 @@ else:
     local resume_phase
     resume_phase=$(python3 -c "
 import json, os
-status_path = os.path.join('$STATE_DIR', 'refactors', '$refactor_id', 'status.json')
+status_path = os.path.join('$STATE_DIR', '$refactor_id', 'status.json')
 if os.path.isfile(status_path):
     with open(status_path) as f:
         d = json.load(f)
@@ -1089,7 +1089,7 @@ DEPLOY_PROMPT_EOF
         run_id=$(jq -r '.run_id' "$STATE_DIR/pipeline.json")
         session_id="${refactor_id}-$(date +%Y%m%d%H%M%S)"
 
-        local session_dir="$STATE_DIR/refactors/$refactor_id/sessions/$session_id"
+        local session_dir="$STATE_DIR/$refactor_id/sessions/$session_id"
         mkdir -p "$session_dir/logs"
 
         local bootstrap_prompt="$session_dir/bootstrap-prompt.md"

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

@@ -113,8 +113,8 @@ def load_json(path):
 
 
 def discover_item_ids(state_dir, subdir):
-    """Return a sorted list of item IDs found in state/{subdir}/."""
-    items_dir = os.path.join(state_dir, subdir)
+    """Return a sorted list of item IDs found directly under the typed state dir."""
+    items_dir = os.path.join(state_dir, subdir) if subdir else state_dir
     if not os.path.isdir(items_dir):
         return []
     ids = []
@@ -363,9 +363,9 @@ def find_task_list(state_dir):
 
 # Pipeline type configurations
 PIPELINE_CONFIG = {
-    "feature": {"subdir": "features", "items_key": "features", "id_label": "feature_id"},
-    "bugfix": {"subdir": "bugs", "items_key": "bugs", "id_label": "bug_id"},
-    "refactor": {"subdir": "refactors", "items_key": "refactors", "id_label": "refactor_id"},
+    "feature": {"subdir": "", "items_key": "features", "id_label": "feature_id"},
+    "bugfix": {"subdir": "", "items_key": "bugs", "id_label": "bug_id"},
+    "refactor": {"subdir": "", "items_key": "refactors", "id_label": "refactor_id"},
 }
 
 

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

@@ -392,9 +392,7 @@ def get_prev_session_status(state_dir, feature_id):
         return "N/A (first run)"
 
     # Try to read the feature status file to find the last session
-    feature_status_path = os.path.join(
-        state_dir, "features", feature_id, "status.json"
-    )
+    feature_status_path = os.path.join(state_dir, feature_id, "status.json")
     if not os.path.isfile(feature_status_path):
         return "N/A (first run)"
 
@@ -409,8 +407,7 @@ def get_prev_session_status(state_dir, feature_id):
         return "N/A (first run)"
 
     # Try to read the last session's session-status.json
-    session_status_path = os.path.join(
-        state_dir, "features", feature_id, "sessions",
+    session_status_path = os.path.join(state_dir, feature_id, "sessions",
         last_session_id, "session-status.json"
     )
     if not os.path.isfile(session_status_path):

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

@@ -220,7 +220,7 @@ def get_prev_session_status(state_dir, bug_id):
     if not state_dir:
         return "N/A (first run)"
 
-    bug_status_path = os.path.join(state_dir, "bugs", bug_id, "status.json")
+    bug_status_path = os.path.join(state_dir, bug_id, "status.json")
     if not os.path.isfile(bug_status_path):
         return "N/A (first run)"
 
@@ -234,8 +234,7 @@ def get_prev_session_status(state_dir, bug_id):
     if not last_session_id:
         return "N/A (first run)"
 
-    session_status_path = os.path.join(
-        state_dir, "bugs", bug_id, "sessions",
+    session_status_path = os.path.join(state_dir, bug_id, "sessions",
         last_session_id, "session-status.json"
     )
     if not os.path.isfile(session_status_path):
@@ -306,7 +305,7 @@ def build_replacements(args, bug, global_context, script_dir):
 
     # Session status path
     session_status_path = os.path.join(
-        project_root, ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+        project_root, ".prizmkit", "state", "bugfix", args.bug_id,
         "sessions", args.session_id, "session-status.json"
     )
 
@@ -371,15 +370,15 @@ def build_replacements(args, bug, global_context, script_dir):
         "{{MAX_LOG_SIZE_HUMAN}}": _format_bytes(max_log_size),
         "{{LOG_MONITOR_POLL_INTERVAL}}": str(poll_interval),
         "{{LOG_MONITOR_STATUS_FILE}}": os.path.join(
-            ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+            ".prizmkit", "state", "bugfix", args.bug_id,
             "sessions", args.session_id, "logs", "log-monitor-status.txt",
         ),
         "{{LOG_MONITOR_BASELINE_FILE}}": os.path.join(
-            ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+            ".prizmkit", "state", "bugfix", args.bug_id,
             "sessions", args.session_id, "logs", "log-monitor-baseline.txt",
         ),
         "{{SESSION_LOG_PATH}}": os.path.join(
-            ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+            ".prizmkit", "state", "bugfix", args.bug_id,
             "sessions", args.session_id, "logs", "session.log",
         ),
         "{{LOG_MONITOR_SCRIPT}}": os.path.join(

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

@@ -375,7 +375,7 @@ def get_prev_session_status(state_dir, refactor_id):
     if not state_dir:
         return "N/A (first run)"
 
-    refactor_status_path = os.path.join(state_dir, "refactors", refactor_id, "status.json")
+    refactor_status_path = os.path.join(state_dir, refactor_id, "status.json")
     try:
         with open(refactor_status_path, "r", encoding="utf-8") as f:
             refactor_status = json.load(f)
@@ -386,8 +386,7 @@ def get_prev_session_status(state_dir, refactor_id):
     if not last_session_id:
         return "N/A (first run)"
 
-    session_status_path = os.path.join(
-        state_dir, "refactors", refactor_id, "sessions",
+    session_status_path = os.path.join(state_dir, refactor_id, "sessions",
         last_session_id, "session-status.json"
     )
     try:
@@ -455,7 +454,7 @@ def build_replacements(args, refactor, refactors, global_context, script_dir):
 
     # Session status path
     session_status_path = os.path.join(
-        project_root, ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+        project_root, ".prizmkit", "state", "refactor", args.refactor_id,
         "sessions", args.session_id, "session-status.json"
     )
 
@@ -531,15 +530,15 @@ def build_replacements(args, refactor, refactors, global_context, script_dir):
         "{{MAX_LOG_SIZE_HUMAN}}": _format_bytes(max_log_size),
         "{{LOG_MONITOR_POLL_INTERVAL}}": str(poll_interval),
         "{{LOG_MONITOR_STATUS_FILE}}": os.path.join(
-            ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+            ".prizmkit", "state", "refactor", args.refactor_id,
             "sessions", args.session_id, "logs", "log-monitor-status.txt",
         ),
         "{{LOG_MONITOR_BASELINE_FILE}}": os.path.join(
-            ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+            ".prizmkit", "state", "refactor", args.refactor_id,
             "sessions", args.session_id, "logs", "log-monitor-baseline.txt",
         ),
         "{{SESSION_LOG_PATH}}": os.path.join(
-            ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+            ".prizmkit", "state", "refactor", args.refactor_id,
             "sessions", args.session_id, "logs", "session.log",
         ),
         "{{LOG_MONITOR_SCRIPT}}": os.path.join(

package/bundled/dev-pipeline/scripts/init-bugfix-pipeline.py

@@ -207,7 +207,7 @@ def create_state_directory(state_dir, bug_list_path, bugs):
     abs_bug_list_path = os.path.abspath(bug_list_path)
     # Store as relative path from state_dir so pipeline.json is portable across machines
     rel_bug_list_path = os.path.relpath(abs_bug_list_path, abs_state_dir)
-    bugs_dir = os.path.join(abs_state_dir, "bugs")
+    bugs_dir = abs_state_dir
 
     now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
     run_id = "bugfix-run-" + datetime.now(timezone.utc).strftime("%Y%m%d%H%M%S")

package/bundled/dev-pipeline/scripts/init-pipeline.py

@@ -242,7 +242,7 @@ def create_state_directory(state_dir, feature_list_path, features):
     abs_feature_list_path = os.path.abspath(feature_list_path)
     # Store as relative path from state_dir so pipeline.json is portable across machines
     rel_feature_list_path = os.path.relpath(abs_feature_list_path, abs_state_dir)
-    features_dir = os.path.join(abs_state_dir, "features")
+    features_dir = abs_state_dir
 
     now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
     run_id = "run-" + datetime.now(timezone.utc).strftime("%Y%m%d%H%M%S")

package/bundled/dev-pipeline/scripts/init-refactor-pipeline.py

@@ -283,7 +283,7 @@ def create_state_directory(state_dir, refactor_list_path, refactors):
     abs_refactor_list_path = os.path.abspath(refactor_list_path)
     # Store as relative path from state_dir so pipeline.json is portable across machines
     rel_refactor_list_path = os.path.relpath(abs_refactor_list_path, abs_state_dir)
-    refactors_dir = os.path.join(abs_state_dir, "refactors")
+    refactors_dir = abs_state_dir
 
     now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
     run_id = "refactor-run-" + datetime.now(timezone.utc).strftime("%Y%m%d%H%M%S")

package/bundled/dev-pipeline/scripts/update-bug-status.py

@@ -92,7 +92,7 @@ def load_bug_status(state_dir, bug_id):
     The 'status' field is NOT included — status lives exclusively
     in bug-fix-list.json.
     """
-    status_path = os.path.join(state_dir, "bugs", bug_id, "status.json")
+    status_path = os.path.join(state_dir, bug_id, "status.json")
     if not os.path.isfile(status_path):
         now = now_iso()
         return {
@@ -133,7 +133,7 @@ def save_bug_status(state_dir, bug_id, status_data):
     """Write the status.json for a bug (runtime fields only)."""
     # Defensively strip status — it belongs in bug-fix-list.json
     status_data.pop("status", None)
-    status_path = os.path.join(state_dir, "bugs", bug_id, "status.json")
+    status_path = os.path.join(state_dir, bug_id, "status.json")
     return write_json_file(status_path, status_data)
 
 
@@ -402,7 +402,7 @@ def cleanup_bug_artifacts(state_dir, bug_id, project_root=None):
     cleaned = []
 
     # 1) Remove all session history
-    sessions_dir = os.path.join(state_dir, "bugs", bug_id, "sessions")
+    sessions_dir = os.path.join(state_dir, bug_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):
@@ -413,7 +413,7 @@ def cleanup_bug_artifacts(state_dir, bug_id, project_root=None):
         cleaned.append("Deleted {} session(s) from {}".format(sessions_deleted, sessions_dir))
 
     # 2) Remove transient files under bug dir (keep status.json)
-    bug_dir = os.path.join(state_dir, "bugs", bug_id)
+    bug_dir = os.path.join(state_dir, bug_id)
     if os.path.isdir(bug_dir):
         for entry in os.listdir(bug_dir):
             if entry == "status.json" or entry == "sessions":
@@ -446,8 +446,7 @@ def cleanup_bug_artifacts(state_dir, bug_id, project_root=None):
 
 
 def load_session_status(state_dir, bug_id, session_id):
-    session_status_path = os.path.join(
-        state_dir, "bugs", bug_id, "sessions",
+    session_status_path = os.path.join(state_dir, bug_id, "sessions",
         session_id, "session-status.json"
     )
     data, err = load_json_file(session_status_path)
@@ -649,7 +648,7 @@ def action_clean(args, bug_list_path, state_dir):
     cleaned = []
 
     # 1. Delete session history
-    sessions_dir = os.path.join(state_dir, "bugs", bug_id, "sessions")
+    sessions_dir = os.path.join(state_dir, bug_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):

package/bundled/dev-pipeline/scripts/update-feature-status.py

@@ -167,9 +167,7 @@ def load_feature_status(state_dir, feature_id):
     The 'status' field is NOT included — status lives exclusively
     in feature-list.json.
     """
-    status_path = os.path.join(
-        state_dir, "features", feature_id, "status.json"
-    )
+    status_path = os.path.join(state_dir, feature_id, "status.json")
     if not os.path.isfile(status_path):
         now = now_iso()
         return {
@@ -210,9 +208,7 @@ def save_feature_status(state_dir, feature_id, status_data):
     """Write the status.json for a feature (runtime fields only)."""
     # Defensively strip status — it belongs in feature-list.json
     status_data.pop("status", None)
-    status_path = os.path.join(
-        state_dir, "features", feature_id, "status.json"
-    )
+    status_path = os.path.join(state_dir, feature_id, "status.json")
     return write_json_file(status_path, status_data)
 
 
@@ -296,7 +292,7 @@ def cleanup_feature_artifacts(feature_list_path, state_dir, feature_id, project_
     cleaned = []
 
     # 1) Remove all session history
-    sessions_dir = os.path.join(state_dir, "features", feature_id, "sessions")
+    sessions_dir = os.path.join(state_dir, feature_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):
@@ -307,7 +303,7 @@ def cleanup_feature_artifacts(feature_list_path, state_dir, feature_id, project_
         cleaned.append("Deleted {} session(s) from {}".format(sessions_deleted, sessions_dir))
 
     # 2) Remove transient files under feature state dir (keep status.json)
-    feature_dir = os.path.join(state_dir, "features", feature_id)
+    feature_dir = os.path.join(state_dir, feature_id)
     if os.path.isdir(feature_dir):
         for entry in os.listdir(feature_dir):
             if entry == "status.json" or entry == "sessions":
@@ -344,8 +340,7 @@ def cleanup_feature_artifacts(feature_list_path, state_dir, feature_id, project_
 
 def load_session_status(state_dir, feature_id, session_id):
     """Load a session's session-status.json file."""
-    session_status_path = os.path.join(
-        state_dir, "features", feature_id, "sessions",
+    session_status_path = os.path.join(state_dir, feature_id, "sessions",
         session_id, "session-status.json"
     )
     data, err = load_json_file(session_status_path)
@@ -785,7 +780,7 @@ def _calc_feature_duration(state_dir, feature_id):
     to the last update time for the calculation.
     Returns None if the duration cannot be calculated.
     """
-    fs_path = os.path.join(state_dir, "features", feature_id, "status.json")
+    fs_path = os.path.join(state_dir, feature_id, "status.json")
     if not os.path.isfile(fs_path):
         return None
     data, err = load_json_file(fs_path)
@@ -1261,7 +1256,7 @@ def action_clean(args, feature_list_path, state_dir):
     cleaned = []
 
     # 1. Delete session history
-    sessions_dir = os.path.join(state_dir, "features", feature_id, "sessions")
+    sessions_dir = os.path.join(state_dir, feature_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):

package/bundled/dev-pipeline/scripts/update-refactor-status.py

@@ -122,7 +122,7 @@ def load_refactor_status(state_dir, refactor_id):
     The 'status' field is NOT included — status lives exclusively
     in refactor-list.json.
     """
-    status_path = os.path.join(state_dir, "refactors", refactor_id, "status.json")
+    status_path = os.path.join(state_dir, refactor_id, "status.json")
     if not os.path.isfile(status_path):
         return _default_status(refactor_id)
     data, err = load_json_file(status_path)
@@ -137,7 +137,7 @@ def save_refactor_status(state_dir, refactor_id, status_data):
     """Write the status.json for a refactor (runtime fields only)."""
     # Defensively strip status — it belongs in refactor-list.json
     status_data.pop("status", None)
-    status_path = os.path.join(state_dir, "refactors", refactor_id, "status.json")
+    status_path = os.path.join(state_dir, refactor_id, "status.json")
     return write_json_file(status_path, status_data)
 
 
@@ -442,7 +442,7 @@ def cleanup_refactor_artifacts(state_dir, refactor_id, project_root=None):
     cleaned = []
 
     # 1) Remove all session history
-    sessions_dir = os.path.join(state_dir, "refactors", refactor_id, "sessions")
+    sessions_dir = os.path.join(state_dir, refactor_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):
@@ -453,7 +453,7 @@ def cleanup_refactor_artifacts(state_dir, refactor_id, project_root=None):
         cleaned.append("Deleted {} session(s) from {}".format(sessions_deleted, sessions_dir))
 
     # 2) Remove transient files under refactor dir (keep status.json)
-    refactor_dir = os.path.join(state_dir, "refactors", refactor_id)
+    refactor_dir = os.path.join(state_dir, refactor_id)
     if os.path.isdir(refactor_dir):
         for entry in os.listdir(refactor_dir):
             if entry == "status.json" or entry == "sessions":
@@ -482,8 +482,7 @@ def cleanup_refactor_artifacts(state_dir, refactor_id, project_root=None):
 
 
 def load_session_status(state_dir, refactor_id, session_id):
-    session_status_path = os.path.join(
-        state_dir, "refactors", refactor_id, "sessions",
+    session_status_path = os.path.join(state_dir, refactor_id, "sessions",
         session_id, "session-status.json"
     )
     data, err = load_json_file(session_status_path)
@@ -797,7 +796,7 @@ def action_clean(args, refactor_list_path, state_dir):
     cleaned = []
 
     # 1. Delete session history
-    sessions_dir = os.path.join(state_dir, "refactors", refactor_id, "sessions")
+    sessions_dir = os.path.join(state_dir, refactor_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):

package/bundled/dev-pipeline/tests/test_auto_skip.py

@@ -38,11 +38,11 @@ def _make_feature_list(features):
 
 def _init_state(tmp_path, feature_ids):
     """Create state dir with status.json for each feature."""
-    state_dir = str(tmp_path / "state")
+    state_dir = str(tmp_path / "state" / "features")
     for fid in feature_ids:
-        feature_dir = os.path.join(state_dir, "features", fid, "sessions")
+        feature_dir = os.path.join(state_dir, fid, "sessions")
         os.makedirs(feature_dir, exist_ok=True)
-        status_path = os.path.join(state_dir, "features", fid, "status.json")
+        status_path = os.path.join(state_dir, fid, "status.json")
         write_json_file(status_path, {
             "feature_id": fid,
             "status": "pending",
@@ -325,7 +325,7 @@ class TestInfraErrorUpdate:
         features = [_make_feature("F-001", "Root", status="in_progress")]
         fl_path = _write_fl(tmp_path, features)
         state_dir = _init_state(tmp_path, ["F-001"])
-        status_path = os.path.join(state_dir, "features", "F-001", "status.json")
+        status_path = os.path.join(state_dir, "F-001", "status.json")
         fs = load_feature_status(state_dir, "F-001")
         fs["retry_count"] = 2
         write_json_file(status_path, fs)
@@ -357,7 +357,7 @@ class TestInfraErrorUpdate:
         features = [_make_feature("F-001", "Root", status="in_progress")]
         fl_path = _write_fl(tmp_path, features)
         state_dir = _init_state(tmp_path, ["F-001"])
-        status_path = os.path.join(state_dir, "features", "F-001", "status.json")
+        status_path = os.path.join(state_dir, "F-001", "status.json")
         fs = load_feature_status(state_dir, "F-001")
         fs["retry_count"] = 1
         fs["infra_error_count"] = 2
@@ -389,7 +389,7 @@ class TestInfraErrorUpdate:
         features = [_make_feature("F-001", "Root", status="failed")]
         fl_path = _write_fl(tmp_path, features)
         state_dir = _init_state(tmp_path, ["F-001"])
-        status_path = os.path.join(state_dir, "features", "F-001", "status.json")
+        status_path = os.path.join(state_dir, "F-001", "status.json")
         fs = load_feature_status(state_dir, "F-001")
         fs["retry_count"] = 3
         fs["infra_error_count"] = 3
@@ -416,7 +416,7 @@ class TestInfraErrorUpdate:
         features = [_make_feature("F-001", "Root", status="failed")]
         fl_path = _write_fl(tmp_path, features)
         state_dir = _init_state(tmp_path, ["F-001"])
-        status_path = os.path.join(state_dir, "features", "F-001", "status.json")
+        status_path = os.path.join(state_dir, "F-001", "status.json")
         fs = load_feature_status(state_dir, "F-001")
         fs["retry_count"] = 3
         fs["infra_error_count"] = 3
@@ -563,7 +563,7 @@ class TestAutoSkipIntegration:
         fl_path = _write_fl(tmp_path, features)
         state_dir = _init_state(tmp_path, ["F-001"])
         # Simulate retry_count = 3
-        fs_path = os.path.join(state_dir, "features", "F-001", "status.json")
+        fs_path = os.path.join(state_dir, "F-001", "status.json")
         with open(fs_path) as f:
             fs = json.load(f)
         fs["retry_count"] = 3

package/bundled/dev-pipeline-windows/lib/pipeline.ps1

@@ -647,7 +647,7 @@ function Invoke-PrizmPipeline {
     }
 
     if ($dryRun) {
-      $statusPath = Join-Path $stateDir "$($idName)s\$CurrentItemId\status.json"
+      $statusPath = Join-Path $stateDir "$CurrentItemId\status.json"
       if (Test-Path $statusPath) {
         try {
           $itemStatus = Get-Content -Raw $statusPath | ConvertFrom-Json
@@ -682,7 +682,7 @@ function Invoke-PrizmPipeline {
     $sessionDir = if ($dryRun) {
       Join-Path ([System.IO.Path]::GetTempPath()) "prizmkit-dry-run\$sessionId"
     } else {
-      Join-Path $stateDir "$($idName)s\$CurrentItemId\sessions\$sessionId"
+      Join-Path $stateDir "$CurrentItemId\sessions\$sessionId"
     }
     $logsDir = Join-Path $sessionDir 'logs'
     New-Item -ItemType Directory -Force -Path $logsDir | Out-Null

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

@@ -113,8 +113,8 @@ def load_json(path):
 
 
 def discover_item_ids(state_dir, subdir):
-    """Return a sorted list of item IDs found in state/{subdir}/."""
-    items_dir = os.path.join(state_dir, subdir)
+    """Return a sorted list of item IDs found directly under the typed state dir."""
+    items_dir = os.path.join(state_dir, subdir) if subdir else state_dir
     if not os.path.isdir(items_dir):
         return []
     ids = []
@@ -363,9 +363,9 @@ def find_task_list(state_dir):
 
 # Pipeline type configurations
 PIPELINE_CONFIG = {
-    "feature": {"subdir": "features", "items_key": "features", "id_label": "feature_id"},
-    "bugfix": {"subdir": "bugs", "items_key": "bugs", "id_label": "bug_id"},
-    "refactor": {"subdir": "refactors", "items_key": "refactors", "id_label": "refactor_id"},
+    "feature": {"subdir": "", "items_key": "features", "id_label": "feature_id"},
+    "bugfix": {"subdir": "", "items_key": "bugs", "id_label": "bug_id"},
+    "refactor": {"subdir": "", "items_key": "refactors", "id_label": "refactor_id"},
 }
 
 

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

@@ -430,9 +430,7 @@ def get_prev_session_status(state_dir, feature_id):
         return "N/A (first run)"
 
     # Try to read the feature status file to find the last session
-    feature_status_path = os.path.join(
-        state_dir, "features", feature_id, "status.json"
-    )
+    feature_status_path = os.path.join(state_dir, feature_id, "status.json")
     if not os.path.isfile(feature_status_path):
         return "N/A (first run)"
 
@@ -447,8 +445,7 @@ def get_prev_session_status(state_dir, feature_id):
         return "N/A (first run)"
 
     # Try to read the last session's session-status.json
-    session_status_path = os.path.join(
-        state_dir, "features", feature_id, "sessions",
+    session_status_path = os.path.join(state_dir, feature_id, "sessions",
         last_session_id, "session-status.json"
     )
     if not os.path.isfile(session_status_path):

package/bundled/dev-pipeline-windows/scripts/generate-bugfix-prompt.py

@@ -221,7 +221,7 @@ def get_prev_session_status(state_dir, bug_id):
     if not state_dir:
         return "N/A (first run)"
 
-    bug_status_path = os.path.join(state_dir, "bugs", bug_id, "status.json")
+    bug_status_path = os.path.join(state_dir, bug_id, "status.json")
     if not os.path.isfile(bug_status_path):
         return "N/A (first run)"
 
@@ -235,8 +235,7 @@ def get_prev_session_status(state_dir, bug_id):
     if not last_session_id:
         return "N/A (first run)"
 
-    session_status_path = os.path.join(
-        state_dir, "bugs", bug_id, "sessions",
+    session_status_path = os.path.join(state_dir, bug_id, "sessions",
         last_session_id, "session-status.json"
     )
     if not os.path.isfile(session_status_path):
@@ -307,7 +306,7 @@ def build_replacements(args, bug, global_context, script_dir):
 
     # Session status path
     session_status_path = os.path.join(
-        project_root, ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+        project_root, ".prizmkit", "state", "bugfix", args.bug_id,
         "sessions", args.session_id, "session-status.json"
     )
 
@@ -372,15 +371,15 @@ def build_replacements(args, bug, global_context, script_dir):
         "{{MAX_LOG_SIZE_HUMAN}}": _format_bytes(max_log_size),
         "{{LOG_MONITOR_POLL_INTERVAL}}": str(poll_interval),
         "{{LOG_MONITOR_STATUS_FILE}}": os.path.join(
-            ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+            ".prizmkit", "state", "bugfix", args.bug_id,
             "sessions", args.session_id, "logs", "log-monitor-status.txt",
         ),
         "{{LOG_MONITOR_BASELINE_FILE}}": os.path.join(
-            ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+            ".prizmkit", "state", "bugfix", args.bug_id,
             "sessions", args.session_id, "logs", "log-monitor-baseline.txt",
         ),
         "{{SESSION_LOG_PATH}}": os.path.join(
-            ".prizmkit", "state", "bugfix", "bugs", args.bug_id,
+            ".prizmkit", "state", "bugfix", args.bug_id,
             "sessions", args.session_id, "logs", "session.log",
         ),
         "{{LOG_MONITOR_SCRIPT}}": os.path.join(

package/bundled/dev-pipeline-windows/scripts/generate-refactor-prompt.py

@@ -376,7 +376,7 @@ def get_prev_session_status(state_dir, refactor_id):
     if not state_dir:
         return "N/A (first run)"
 
-    refactor_status_path = os.path.join(state_dir, "refactors", refactor_id, "status.json")
+    refactor_status_path = os.path.join(state_dir, refactor_id, "status.json")
     try:
         with open(refactor_status_path, "r", encoding="utf-8") as f:
             refactor_status = json.load(f)
@@ -387,8 +387,7 @@ def get_prev_session_status(state_dir, refactor_id):
     if not last_session_id:
         return "N/A (first run)"
 
-    session_status_path = os.path.join(
-        state_dir, "refactors", refactor_id, "sessions",
+    session_status_path = os.path.join(state_dir, refactor_id, "sessions",
         last_session_id, "session-status.json"
     )
     try:
@@ -456,7 +455,7 @@ def build_replacements(args, refactor, refactors, global_context, script_dir):
 
     # Session status path
     session_status_path = os.path.join(
-        project_root, ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+        project_root, ".prizmkit", "state", "refactor", args.refactor_id,
         "sessions", args.session_id, "session-status.json"
     )
 
@@ -532,15 +531,15 @@ def build_replacements(args, refactor, refactors, global_context, script_dir):
         "{{MAX_LOG_SIZE_HUMAN}}": _format_bytes(max_log_size),
         "{{LOG_MONITOR_POLL_INTERVAL}}": str(poll_interval),
         "{{LOG_MONITOR_STATUS_FILE}}": os.path.join(
-            ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+            ".prizmkit", "state", "refactor", args.refactor_id,
             "sessions", args.session_id, "logs", "log-monitor-status.txt",
         ),
         "{{LOG_MONITOR_BASELINE_FILE}}": os.path.join(
-            ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+            ".prizmkit", "state", "refactor", args.refactor_id,
             "sessions", args.session_id, "logs", "log-monitor-baseline.txt",
         ),
         "{{SESSION_LOG_PATH}}": os.path.join(
-            ".prizmkit", "state", "refactor", "refactors", args.refactor_id,
+            ".prizmkit", "state", "refactor", args.refactor_id,
             "sessions", args.session_id, "logs", "session.log",
         ),
         "{{LOG_MONITOR_SCRIPT}}": os.path.join(

package/bundled/dev-pipeline-windows/scripts/init-bugfix-pipeline.py

@@ -207,7 +207,7 @@ def create_state_directory(state_dir, bug_list_path, bugs):
     abs_bug_list_path = os.path.abspath(bug_list_path)
     # Store as relative path from state_dir so pipeline.json is portable across machines
     rel_bug_list_path = os.path.relpath(abs_bug_list_path, abs_state_dir)
-    bugs_dir = os.path.join(abs_state_dir, "bugs")
+    bugs_dir = abs_state_dir
 
     now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
     run_id = "bugfix-run-" + datetime.now(timezone.utc).strftime("%Y%m%d%H%M%S")

package/bundled/dev-pipeline-windows/scripts/init-pipeline.py

@@ -242,7 +242,7 @@ def create_state_directory(state_dir, feature_list_path, features):
     abs_feature_list_path = os.path.abspath(feature_list_path)
     # Store as relative path from state_dir so pipeline.json is portable across machines
     rel_feature_list_path = os.path.relpath(abs_feature_list_path, abs_state_dir)
-    features_dir = os.path.join(abs_state_dir, "features")
+    features_dir = abs_state_dir
 
     now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
     run_id = "run-" + datetime.now(timezone.utc).strftime("%Y%m%d%H%M%S")

package/bundled/dev-pipeline-windows/scripts/init-refactor-pipeline.py

@@ -283,7 +283,7 @@ def create_state_directory(state_dir, refactor_list_path, refactors):
     abs_refactor_list_path = os.path.abspath(refactor_list_path)
     # Store as relative path from state_dir so pipeline.json is portable across machines
     rel_refactor_list_path = os.path.relpath(abs_refactor_list_path, abs_state_dir)
-    refactors_dir = os.path.join(abs_state_dir, "refactors")
+    refactors_dir = abs_state_dir
 
     now = datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
     run_id = "refactor-run-" + datetime.now(timezone.utc).strftime("%Y%m%d%H%M%S")

package/bundled/dev-pipeline-windows/scripts/update-bug-status.py

@@ -92,7 +92,7 @@ def load_bug_status(state_dir, bug_id):
     The 'status' field is NOT included — status lives exclusively
     in bug-fix-list.json.
     """
-    status_path = os.path.join(state_dir, "bugs", bug_id, "status.json")
+    status_path = os.path.join(state_dir, bug_id, "status.json")
     if not os.path.isfile(status_path):
         now = now_iso()
         return {
@@ -133,7 +133,7 @@ def save_bug_status(state_dir, bug_id, status_data):
     """Write the status.json for a bug (runtime fields only)."""
     # Defensively strip status — it belongs in bug-fix-list.json
     status_data.pop("status", None)
-    status_path = os.path.join(state_dir, "bugs", bug_id, "status.json")
+    status_path = os.path.join(state_dir, bug_id, "status.json")
     return write_json_file(status_path, status_data)
 
 
@@ -402,7 +402,7 @@ def cleanup_bug_artifacts(state_dir, bug_id, project_root=None):
     cleaned = []
 
     # 1) Remove all session history
-    sessions_dir = os.path.join(state_dir, "bugs", bug_id, "sessions")
+    sessions_dir = os.path.join(state_dir, bug_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):
@@ -413,7 +413,7 @@ def cleanup_bug_artifacts(state_dir, bug_id, project_root=None):
         cleaned.append("Deleted {} session(s) from {}".format(sessions_deleted, sessions_dir))
 
     # 2) Remove transient files under bug dir (keep status.json)
-    bug_dir = os.path.join(state_dir, "bugs", bug_id)
+    bug_dir = os.path.join(state_dir, bug_id)
     if os.path.isdir(bug_dir):
         for entry in os.listdir(bug_dir):
             if entry == "status.json" or entry == "sessions":
@@ -446,8 +446,7 @@ def cleanup_bug_artifacts(state_dir, bug_id, project_root=None):
 
 
 def load_session_status(state_dir, bug_id, session_id):
-    session_status_path = os.path.join(
-        state_dir, "bugs", bug_id, "sessions",
+    session_status_path = os.path.join(state_dir, bug_id, "sessions",
         session_id, "session-status.json"
     )
     data, err = load_json_file(session_status_path)
@@ -649,7 +648,7 @@ def action_clean(args, bug_list_path, state_dir):
     cleaned = []
 
     # 1. Delete session history
-    sessions_dir = os.path.join(state_dir, "bugs", bug_id, "sessions")
+    sessions_dir = os.path.join(state_dir, bug_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):

package/bundled/dev-pipeline-windows/scripts/update-feature-status.py

@@ -167,9 +167,7 @@ def load_feature_status(state_dir, feature_id):
     The 'status' field is NOT included — status lives exclusively
     in feature-list.json.
     """
-    status_path = os.path.join(
-        state_dir, "features", feature_id, "status.json"
-    )
+    status_path = os.path.join(state_dir, feature_id, "status.json")
     if not os.path.isfile(status_path):
         now = now_iso()
         return {
@@ -210,9 +208,7 @@ def save_feature_status(state_dir, feature_id, status_data):
     """Write the status.json for a feature (runtime fields only)."""
     # Defensively strip status — it belongs in feature-list.json
     status_data.pop("status", None)
-    status_path = os.path.join(
-        state_dir, "features", feature_id, "status.json"
-    )
+    status_path = os.path.join(state_dir, feature_id, "status.json")
     return write_json_file(status_path, status_data)
 
 
@@ -296,7 +292,7 @@ def cleanup_feature_artifacts(feature_list_path, state_dir, feature_id, project_
     cleaned = []
 
     # 1) Remove all session history
-    sessions_dir = os.path.join(state_dir, "features", feature_id, "sessions")
+    sessions_dir = os.path.join(state_dir, feature_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):
@@ -307,7 +303,7 @@ def cleanup_feature_artifacts(feature_list_path, state_dir, feature_id, project_
         cleaned.append("Deleted {} session(s) from {}".format(sessions_deleted, sessions_dir))
 
     # 2) Remove transient files under feature state dir (keep status.json)
-    feature_dir = os.path.join(state_dir, "features", feature_id)
+    feature_dir = os.path.join(state_dir, feature_id)
     if os.path.isdir(feature_dir):
         for entry in os.listdir(feature_dir):
             if entry == "status.json" or entry == "sessions":
@@ -344,8 +340,7 @@ def cleanup_feature_artifacts(feature_list_path, state_dir, feature_id, project_
 
 def load_session_status(state_dir, feature_id, session_id):
     """Load a session's session-status.json file."""
-    session_status_path = os.path.join(
-        state_dir, "features", feature_id, "sessions",
+    session_status_path = os.path.join(state_dir, feature_id, "sessions",
         session_id, "session-status.json"
     )
     data, err = load_json_file(session_status_path)
@@ -785,7 +780,7 @@ def _calc_feature_duration(state_dir, feature_id):
     to the last update time for the calculation.
     Returns None if the duration cannot be calculated.
     """
-    fs_path = os.path.join(state_dir, "features", feature_id, "status.json")
+    fs_path = os.path.join(state_dir, feature_id, "status.json")
     if not os.path.isfile(fs_path):
         return None
     data, err = load_json_file(fs_path)
@@ -1261,7 +1256,7 @@ def action_clean(args, feature_list_path, state_dir):
     cleaned = []
 
     # 1. Delete session history
-    sessions_dir = os.path.join(state_dir, "features", feature_id, "sessions")
+    sessions_dir = os.path.join(state_dir, feature_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):

package/bundled/dev-pipeline-windows/scripts/update-refactor-status.py

@@ -122,7 +122,7 @@ def load_refactor_status(state_dir, refactor_id):
     The 'status' field is NOT included — status lives exclusively
     in refactor-list.json.
     """
-    status_path = os.path.join(state_dir, "refactors", refactor_id, "status.json")
+    status_path = os.path.join(state_dir, refactor_id, "status.json")
     if not os.path.isfile(status_path):
         return _default_status(refactor_id)
     data, err = load_json_file(status_path)
@@ -137,7 +137,7 @@ def save_refactor_status(state_dir, refactor_id, status_data):
     """Write the status.json for a refactor (runtime fields only)."""
     # Defensively strip status — it belongs in refactor-list.json
     status_data.pop("status", None)
-    status_path = os.path.join(state_dir, "refactors", refactor_id, "status.json")
+    status_path = os.path.join(state_dir, refactor_id, "status.json")
     return write_json_file(status_path, status_data)
 
 
@@ -442,7 +442,7 @@ def cleanup_refactor_artifacts(state_dir, refactor_id, project_root=None):
     cleaned = []
 
     # 1) Remove all session history
-    sessions_dir = os.path.join(state_dir, "refactors", refactor_id, "sessions")
+    sessions_dir = os.path.join(state_dir, refactor_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):
@@ -453,7 +453,7 @@ def cleanup_refactor_artifacts(state_dir, refactor_id, project_root=None):
         cleaned.append("Deleted {} session(s) from {}".format(sessions_deleted, sessions_dir))
 
     # 2) Remove transient files under refactor dir (keep status.json)
-    refactor_dir = os.path.join(state_dir, "refactors", refactor_id)
+    refactor_dir = os.path.join(state_dir, refactor_id)
     if os.path.isdir(refactor_dir):
         for entry in os.listdir(refactor_dir):
             if entry == "status.json" or entry == "sessions":
@@ -482,8 +482,7 @@ def cleanup_refactor_artifacts(state_dir, refactor_id, project_root=None):
 
 
 def load_session_status(state_dir, refactor_id, session_id):
-    session_status_path = os.path.join(
-        state_dir, "refactors", refactor_id, "sessions",
+    session_status_path = os.path.join(state_dir, refactor_id, "sessions",
         session_id, "session-status.json"
     )
     data, err = load_json_file(session_status_path)
@@ -797,7 +796,7 @@ def action_clean(args, refactor_list_path, state_dir):
     cleaned = []
 
     # 1. Delete session history
-    sessions_dir = os.path.join(state_dir, "refactors", refactor_id, "sessions")
+    sessions_dir = os.path.join(state_dir, refactor_id, "sessions")
     sessions_deleted = 0
     if os.path.isdir(sessions_dir):
         for entry in os.listdir(sessions_dir):

package/bundled/skills/_metadata.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.1.97",
+  "version": "1.1.99",
   "skills": {
     "prizm-kit": {
       "description": "Full-lifecycle dev toolkit. Covers spec-driven development, Prizm context docs, code quality, debugging, deployment, and knowledge management.",

package/bundled/skills/bugfix-pipeline-launcher/SKILL.md

@@ -245,9 +245,9 @@ Detect user intent from their message, then follow the corresponding workflow:
 4. **For per-bug session logs** (when user asks about a specific bug):
    ```bash
    # Check bug status for last session ID
-   cat .prizmkit/state/bugfix/bugs/<BUG_ID>/status.json 2>/dev/null
+   cat .prizmkit/state/bugfix/<BUG_ID>/status.json 2>/dev/null
    # Then tail that bug's session log
-   tail -100 .prizmkit/state/bugfix/bugs/<BUG_ID>/sessions/<SESSION_ID>/logs/session.log
+   tail -100 .prizmkit/state/bugfix/<BUG_ID>/sessions/<SESSION_ID>/logs/session.log
    ```
 
 ---

package/bundled/skills/feature-pipeline-launcher/SKILL.md

@@ -285,9 +285,9 @@ Detect user intent from their message, then follow the corresponding workflow:
 4. **For per-feature session logs** (when user asks about a specific feature):
    ```bash
    # Check feature status for last session ID
-   cat .prizmkit/state/features/features/<FEATURE_ID>/status.json 2>/dev/null
+   cat .prizmkit/state/features/<FEATURE_ID>/status.json 2>/dev/null
    # Then tail that feature's session log
-   tail -100 .prizmkit/state/features/features/<FEATURE_ID>/sessions/<SESSION_ID>/logs/session.log
+   tail -100 .prizmkit/state/features/<FEATURE_ID>/sessions/<SESSION_ID>/logs/session.log
    ```
 
 ---

package/bundled/skills/recovery-workflow/SKILL.md

@@ -48,8 +48,8 @@ Pipeline commands (for reference — Phase 1.3 will present these as a selectabl
 | Workflow | Branch Pattern | Key Artifacts |
 |----------|---------------|---------------|
 | bug-fix-workflow | `fix/<BUG_ID>-*` | `.prizmkit/bugfix/<BUG_ID>/fix-plan.md`, `fix-report.md` |
-| feature-workflow | `feat/*` | `.prizmkit/plans/feature-list.json`, `.prizmkit/state/features/features/` |
-| refactor-workflow | `refactor/*` | `.prizmkit/plans/refactor-list.json`, `.prizmkit/state/refactor/refactors/` |
+| feature-workflow | `feat/*` | `.prizmkit/plans/feature-list.json`, `.prizmkit/state/features/` |
+| refactor-workflow | `refactor/*` | `.prizmkit/plans/refactor-list.json`, `.prizmkit/state/refactor/` |
 
 ---
 

package/bundled/skills/recovery-workflow/evals/evals.json

@@ -23,7 +23,7 @@
       "name": "feature-list-exists",
       "prompt": "resume",
       "expected_output": "Should auto-detect feature-workflow from .prizmkit/plans/feature-list.json. Should detect .prizmkit/plans/feature-list.json exists but no pipeline state → infer Phase 3 (Launch). Should invoke feature-pipeline-launcher to start the pipeline.",
-      "setup_description": "On main branch, create .prizmkit/plans/feature-list.json with 3 features. No .prizmkit/state/features/features/ directory.",
+      "setup_description": "On main branch, create .prizmkit/plans/feature-list.json with 3 features. No .prizmkit/state/features/ directory.",
       "files": []
     },
     {
@@ -31,7 +31,7 @@
       "name": "refactor-monitoring",
       "prompt": "pick up where it left off",
       "expected_output": "Should auto-detect refactor-workflow from .prizmkit/plans/refactor-list.json + pipeline state. Should infer Phase 4 (Monitor). Should check pipeline status and report results.",
-      "setup_description": "On main branch, create .prizmkit/plans/refactor-list.json with 2 items. Create .prizmkit/state/refactor/refactors/ with status files showing 1 completed, 1 in-progress.",
+      "setup_description": "On main branch, create .prizmkit/plans/refactor-list.json with 2 items. Create .prizmkit/state/refactor/ with status files showing 1 completed, 1 in-progress.",
       "files": []
     },
     {

package/bundled/skills/refactor-pipeline-launcher/SKILL.md

@@ -288,9 +288,9 @@ Detect user intent from their message, then follow the corresponding workflow:
 4. **For per-refactor session logs** (when user asks about a specific refactor):
    ```bash
    # Check refactor status for last session ID
-   cat .prizmkit/state/refactor/refactors/<REFACTOR_ID>/status.json 2>/dev/null
+   cat .prizmkit/state/refactor/<REFACTOR_ID>/status.json 2>/dev/null
    # Then tail that refactor's session log
-   tail -100 .prizmkit/state/refactor/refactors/<REFACTOR_ID>/sessions/<SESSION_ID>/logs/session.log
+   tail -100 .prizmkit/state/refactor/<REFACTOR_ID>/sessions/<SESSION_ID>/logs/session.log
    ```
 
 ---

package/bundled/skills-windows/bugfix-pipeline-launcher/SKILL.md

@@ -271,9 +271,9 @@ Detect user intent from their message, then follow the corresponding workflow:
 4. **For per-bug session logs** (when user asks about a specific bug):
    ```powershell
    # Check bug status for last session ID
-   Get-Content .prizmkit/state/bugfix/bugs/<BUG_ID>/status.json -ErrorAction SilentlyContinue
+   Get-Content .prizmkit/state/bugfix/<BUG_ID>/status.json -ErrorAction SilentlyContinue
    # Then tail that bug's session log
-   Get-Content -Tail 100 .prizmkit/state/bugfix/bugs/<BUG_ID>/sessions/<SESSION_ID>/logs/session.log
+   Get-Content -Tail 100 .prizmkit/state/bugfix/<BUG_ID>/sessions/<SESSION_ID>/logs/session.log
    ```
 
 ---

package/bundled/skills-windows/feature-pipeline-launcher/SKILL.md

@@ -312,9 +312,9 @@ Detect user intent from their message, then follow the corresponding workflow:
 4. **For per-feature session logs** (when user asks about a specific feature):
    ```powershell
    # Check feature status for last session ID
-   Get-Content .prizmkit/state/features/features/<FEATURE_ID>/status.json -ErrorAction SilentlyContinue
+   Get-Content .prizmkit/state/features/<FEATURE_ID>/status.json -ErrorAction SilentlyContinue
    # Then tail that feature's session log
-   Get-Content -Tail 100 .prizmkit/state/features/features/<FEATURE_ID>/sessions/<SESSION_ID>/logs/session.log
+   Get-Content -Tail 100 .prizmkit/state/features/<FEATURE_ID>/sessions/<SESSION_ID>/logs/session.log
    ```
 
 ---

package/bundled/skills-windows/recovery-workflow/SKILL.md

@@ -48,8 +48,8 @@ Pipeline commands (for reference — Phase 1.3 will present these as a selectabl
 | Workflow | Branch Pattern | Key Artifacts |
 |----------|---------------|---------------|
 | bug-fix-workflow | `fix/<BUG_ID>-*` | `.prizmkit/bugfix/<BUG_ID>/fix-plan.md`, `fix-report.md` |
-| feature-workflow | `feat/*` | `.prizmkit/plans/feature-list.json`, `.prizmkit/state/features/features/` |
-| refactor-workflow | `refactor/*` | `.prizmkit/plans/refactor-list.json`, `.prizmkit/state/refactor/refactors/` |
+| feature-workflow | `feat/*` | `.prizmkit/plans/feature-list.json`, `.prizmkit/state/features/` |
+| refactor-workflow | `refactor/*` | `.prizmkit/plans/refactor-list.json`, `.prizmkit/state/refactor/` |
 
 ---
 

package/bundled/skills-windows/recovery-workflow/evals/evals.json

@@ -23,7 +23,7 @@
       "name": "feature-list-exists",
       "prompt": "resume",
       "expected_output": "Should auto-detect feature-workflow from .prizmkit/plans/feature-list.json. Should detect .prizmkit/plans/feature-list.json exists but no pipeline state → infer Phase 3 (Launch). Should invoke feature-pipeline-launcher to start the pipeline.",
-      "setup_description": "On main branch, create .prizmkit/plans/feature-list.json with 3 features. No .prizmkit/state/features/features/ directory.",
+      "setup_description": "On main branch, create .prizmkit/plans/feature-list.json with 3 features. No .prizmkit/state/features/ directory.",
       "files": []
     },
     {
@@ -31,7 +31,7 @@
       "name": "refactor-monitoring",
       "prompt": "pick up where it left off",
       "expected_output": "Should auto-detect refactor-workflow from .prizmkit/plans/refactor-list.json + pipeline state. Should infer Phase 4 (Monitor). Should check pipeline status and report results.",
-      "setup_description": "On main branch, create .prizmkit/plans/refactor-list.json with 2 items. Create .prizmkit/state/refactor/refactors/ with status files showing 1 completed, 1 in-progress.",
+      "setup_description": "On main branch, create .prizmkit/plans/refactor-list.json with 2 items. Create .prizmkit/state/refactor/ with status files showing 1 completed, 1 in-progress.",
       "files": []
     },
     {

package/bundled/skills-windows/refactor-pipeline-launcher/SKILL.md

@@ -311,9 +311,9 @@ Detect user intent from their message, then follow the corresponding workflow:
 4. **For per-refactor session logs** (when user asks about a specific refactor):
    ```powershell
    # Check refactor status for last session ID
-   Get-Content .prizmkit/state/refactor/refactors/<REFACTOR_ID>/status.json -ErrorAction SilentlyContinue
+   Get-Content .prizmkit/state/refactor/<REFACTOR_ID>/status.json -ErrorAction SilentlyContinue
    # Then tail that refactor's session log
-   Get-Content -Tail 100 .prizmkit/state/refactor/refactors/<REFACTOR_ID>/sessions/<SESSION_ID>/logs/session.log
+   Get-Content -Tail 100 .prizmkit/state/refactor/<REFACTOR_ID>/sessions/<SESSION_ID>/logs/session.log
    ```
 
 ---

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "prizmkit",
-  "version": "1.1.97",
+  "version": "1.1.99",
   "description": "Create a new PrizmKit-powered project with clean initialization — no framework dev files, just what you need.",
   "type": "module",
   "bin": {