fix(ci): require clean probe exit for Windows shell/bash detection; add pyyaml dev dep

Co-Authored-By: Devin AI <158243242+devin-ai-integration[bot]@users.noreply.github.com>

package-lock.json

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-    "node_modules/glob/node_modules/balanced-match": {
-      "version": "4.0.4",
-      "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-4.0.4.tgz",
-      "integrity": "sha512-BLrgEcRTwX2o6gGxGOCNyMvGSp35YofuYzw9h1IMTRmKqttAZZVU67bdb9Pr2vUHA8+j3i2tJfjO6C6+4myGTA==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": "18 || 20 || >=22"
-      }
-    },
-    "node_modules/glob/node_modules/brace-expansion": {
-      "version": "5.0.6",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-5.0.6.tgz",
-      "integrity": "sha512-kLpxurY4Z4r9sgMsyG0Z9uzsBlgiU/EFKhj/h91/8yHu0edo7XuixOIH3VcJ8kkxs6/jPzoI6U9Vj3WqbMQ94g==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "balanced-match": "^4.0.2"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      }
-    },
-    "node_modules/glob/node_modules/minimatch": {
-      "version": "10.2.5",
-      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.2.5.tgz",
-      "integrity": "sha512-MULkVLfKGYDFYejP07QOurDLLQpcjk7Fw+7jXS2R2czRQzR56yHRveU5NDJEOviH+hETZKSkIk5c+T23GjFUMg==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "brace-expansion": "^5.0.5"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
     "node_modules/globals": {
       "version": "17.4.0",
       "resolved": "https://registry.npmjs.org/globals/-/globals-17.4.0.tgz",
@@ -1445,23 +1324,6 @@
         "node": ">= 4"
       }
     },
-    "node_modules/import-fresh": {
-      "version": "3.3.1",
-      "resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.1.tgz",
-      "integrity": "sha512-TR3KfrTZTYLPB6jUjfx6MF9WcWrHL9su5TObK4ZkYgBdWKPOFoSoQIdEuTuR82pmtxH2spWG9h6etwfr1pLBqQ==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "parent-module": "^1.0.0",
-        "resolve-from": "^4.0.0"
-      },
-      "engines": {
-        "node": ">=6"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
     "node_modules/imurmurhash": {
       "version": "0.1.4",
       "resolved": "https://registry.npmjs.org/imurmurhash/-/imurmurhash-0.1.4.tgz",
@@ -1763,13 +1625,6 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
-    "node_modules/lodash.merge": {
-      "version": "4.6.2",
-      "resolved": "https://registry.npmjs.org/lodash.merge/-/lodash.merge-4.6.2.tgz",
-      "integrity": "sha512-0KpjqXRVvrYyCsX1swR/XTK0va6VQkQM6MNo7PqW77ByjAhoARA8EfrP1N4+KlKj8YS0ZUCtRT/YUuhyYDujIQ==",
-      "dev": true,
-      "license": "MIT"
-    },
     "node_modules/lru-cache": {
       "version": "11.2.7",
       "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.2.7.tgz",
@@ -1875,29 +1730,6 @@
         "node": ">=20"
       }
     },
-    "node_modules/markdownlint-cli/node_modules/balanced-match": {
-      "version": "4.0.4",
-      "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-4.0.4.tgz",
-      "integrity": "sha512-BLrgEcRTwX2o6gGxGOCNyMvGSp35YofuYzw9h1IMTRmKqttAZZVU67bdb9Pr2vUHA8+j3i2tJfjO6C6+4myGTA==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": "18 || 20 || >=22"
-      }
-    },
-    "node_modules/markdownlint-cli/node_modules/brace-expansion": {
-      "version": "5.0.6",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-5.0.6.tgz",
-      "integrity": "sha512-kLpxurY4Z4r9sgMsyG0Z9uzsBlgiU/EFKhj/h91/8yHu0edo7XuixOIH3VcJ8kkxs6/jPzoI6U9Vj3WqbMQ94g==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "balanced-match": "^4.0.2"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      }
-    },
     "node_modules/markdownlint-cli/node_modules/ignore": {
       "version": "7.0.5",
       "resolved": "https://registry.npmjs.org/ignore/-/ignore-7.0.5.tgz",
@@ -1908,22 +1740,6 @@
         "node": ">= 4"
       }
     },
-    "node_modules/markdownlint-cli/node_modules/minimatch": {
-      "version": "10.2.5",
-      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.2.5.tgz",
-      "integrity": "sha512-MULkVLfKGYDFYejP07QOurDLLQpcjk7Fw+7jXS2R2czRQzR56yHRveU5NDJEOviH+hETZKSkIk5c+T23GjFUMg==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "brace-expansion": "^5.0.5"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
     "node_modules/mdurl": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/mdurl/-/mdurl-2.0.0.tgz",
@@ -2467,15 +2283,19 @@
       "license": "MIT"
     },
     "node_modules/minimatch": {
-      "version": "3.1.5",
+      "version": "10.2.5",
-      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.5.tgz",
+      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.2.5.tgz",
-      "integrity": "sha512-VgjWUsnnT6n+NUk6eZq77zeFdpW2LWDzP6zFGrCbHXiYNul5Dzqk2HHQ5uFH2DNW5Xbp8+jVzaeNt94ssEEl4w==",
+      "integrity": "sha512-MULkVLfKGYDFYejP07QOurDLLQpcjk7Fw+7jXS2R2czRQzR56yHRveU5NDJEOviH+hETZKSkIk5c+T23GjFUMg==",
       "dev": true,
+      "license": "BlueOak-1.0.0",
       "dependencies": {
-        "brace-expansion": "^1.1.7"
+        "brace-expansion": "^5.0.5"
       },
       "engines": {
-        "node": "*"
+        "node": "18 || 20 || >=22"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/isaacs"
       }
     },
     "node_modules/minimist": {
@@ -2618,19 +2438,6 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
-    "node_modules/parent-module": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz",
-      "integrity": "sha512-GQ2EWRpQV8/o+Aw8YqtfZZPfNRWZYkbidE9k5rpl/hC3vtHHBfGm2Ifi6qWV+coDGkrUKZAxE3Lot5kcsRlh+g==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "callsites": "^3.0.0"
-      },
-      "engines": {
-        "node": ">=6"
-      }
-    },
     "node_modules/parse-entities": {
       "version": "4.0.2",
       "resolved": "https://registry.npmjs.org/parse-entities/-/parse-entities-4.0.2.tgz",
@@ -2766,16 +2573,6 @@
         "node": ">=0.10.0"
       }
     },
-    "node_modules/resolve-from": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-4.0.0.tgz",
-      "integrity": "sha512-pb/MYmXstAkysRFx8piNI1tGFNQIFA3vkE3Gq4EuA1dF6gHp/+vgZqsCGJapvy8N3Q+4o7FwvquPJcnZ7RYy4g==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=4"
-      }
-    },
     "node_modules/run-con": {
       "version": "1.3.2",
       "resolved": "https://registry.npmjs.org/run-con/-/run-con-1.3.2.tgz",
@@ -2934,45 +2731,6 @@
         "node": "20 || >=22"
       }
     },
-    "node_modules/test-exclude/node_modules/balanced-match": {
-      "version": "4.0.4",
-      "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-4.0.4.tgz",
-      "integrity": "sha512-BLrgEcRTwX2o6gGxGOCNyMvGSp35YofuYzw9h1IMTRmKqttAZZVU67bdb9Pr2vUHA8+j3i2tJfjO6C6+4myGTA==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": "18 || 20 || >=22"
-      }
-    },
-    "node_modules/test-exclude/node_modules/brace-expansion": {
-      "version": "5.0.6",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-5.0.6.tgz",
-      "integrity": "sha512-kLpxurY4Z4r9sgMsyG0Z9uzsBlgiU/EFKhj/h91/8yHu0edo7XuixOIH3VcJ8kkxs6/jPzoI6U9Vj3WqbMQ94g==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "balanced-match": "^4.0.2"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      }
-    },
-    "node_modules/test-exclude/node_modules/minimatch": {
-      "version": "10.2.5",
-      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.2.5.tgz",
-      "integrity": "sha512-MULkVLfKGYDFYejP07QOurDLLQpcjk7Fw+7jXS2R2czRQzR56yHRveU5NDJEOviH+hETZKSkIk5c+T23GjFUMg==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "brace-expansion": "^5.0.5"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
     "node_modules/tinyglobby": {
       "version": "0.2.15",
       "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.15.tgz",

pyproject.toml

@@ -31,6 +31,7 @@ dev = [
     "pytest-mock>=3.12",
     "ruff>=0.4",
     "mypy>=2.1.0",
+    "pyyaml>=6.0",
 ]
 
 [project.urls]

scripts/hooks/plugin-hook-bootstrap.js

@@ -97,7 +97,10 @@ function findShellBinary() {
       windowsHide: true,
       timeout: 30000,
     });
-    if (!probe.error) {
+    // A candidate is only usable if it both spawns AND exits cleanly. The
+    // Windows System32 bash.exe WSL launcher spawns without error but exits
+    // non-zero when no distro is installed, so !probe.error alone is not enough.
+    if (!probe.error && probe.status === 0) {
       _cachedShell = candidate;
       return _cachedShell;
     }
@@ -118,7 +121,9 @@ function findBashBinary() {
 
   for (const candidate of candidates) {
     const probe = spawnSync(candidate, ['-c', ':'], { stdio: 'ignore', windowsHide: true, timeout: 30000 });
-    if (!probe.error) {
+    // Require a clean exit, not just a successful spawn: the Windows System32
+    // bash.exe WSL stub spawns fine but exits non-zero with no distro installed.
+    if (!probe.error && probe.status === 0) {
       _cachedBash = candidate;
       return _cachedBash;
     }

scripts/lib/install/apply.js

@@ -5,6 +5,29 @@ const path = require('path');
 
 const { writeInstallState } = require('../install-state');
 const { filterMcpConfig, parseDisabledMcpServers } = require('../mcp-config');
+const { rewriteNamespaceLinks } = require('./rewrite-namespace-links');
+
+const CLAUDE_ECC_NAMESPACE = 'ecc';
+
+// Claude home/project installs inject `skills/ecc/` and `rules/ecc/`. Markdown
+// copied under those namespaced roots may carry source-relative links to a
+// sibling top-level dir that break post-install; rewrite them on copy.
+function getNamespaceLinkRewrite(plan, destinationPath) {
+  if (!plan.adapter || (plan.adapter.target !== 'claude' && plan.adapter.target !== 'claude-project')) {
+    return null;
+  }
+  if (!plan.targetRoot || !destinationPath.toLowerCase().endsWith('.md')) {
+    return null;
+  }
+  const namespacedRoots = [
+    path.join(plan.targetRoot, 'skills', CLAUDE_ECC_NAMESPACE) + path.sep,
+    path.join(plan.targetRoot, 'rules', CLAUDE_ECC_NAMESPACE) + path.sep,
+  ];
+  if (!namespacedRoots.some(root => destinationPath.startsWith(root))) {
+    return null;
+  }
+  return CLAUDE_ECC_NAMESPACE;
+}
 
 function readJsonObject(filePath, label) {
   let parsed;
@@ -149,6 +172,16 @@ function applyInstallPlan(plan) {
       continue;
     }
 
+    const namespace = operation.kind === 'copy-file'
+      ? getNamespaceLinkRewrite(plan, operation.destinationPath)
+      : null;
+    if (namespace) {
+      const original = fs.readFileSync(operation.sourcePath, 'utf8');
+      const rewritten = rewriteNamespaceLinks(original, namespace);
+      fs.writeFileSync(operation.destinationPath, rewritten, 'utf8');
+      continue;
+    }
+
     fs.copyFileSync(operation.sourcePath, operation.destinationPath);
   }
 

scripts/lib/install/rewrite-namespace-links.js

@@ -0,0 +1,48 @@
+'use strict';
+
+// The Claude home/project installers inject a namespace segment into the
+// destination layout: `skills/` -> `skills/<ns>/` and `rules/` -> `rules/<ns>/`.
+// Skills that link to a sibling top-level dir using a source-relative path
+// (e.g. `../../rules/react/hooks.md`) break after install, because the extra
+// `<ns>/` level changes what `../../` resolves to and the target dir is itself
+// namespaced.
+//
+// This rewrites such links so they remain valid post-install: prepend one `../`
+// (to climb out of the injected namespace level) and insert the namespace
+// segment after the managed top-level dir name. Only links that climb with at
+// least two `../` and reference a namespaced managed dir (`rules`/`skills`) are
+// touched; intra-skill links (a single `../`) and absolute/bare paths are left
+// alone.
+
+const NAMESPACED_DIRS = ['rules', 'skills'];
+
+function buildLinkPattern() {
+  const dirs = NAMESPACED_DIRS.join('|');
+  // group 1: the `../` climb (>= 2), group 2: managed dir, group 3: trailing `/`
+  return new RegExp(`((?:\\.\\./){2,})(${dirs})(/)`, 'g');
+}
+
+/**
+ * Rewrite source-relative links in a namespaced skill/rule markdown file so they
+ * resolve correctly after the installer injects `<namespace>/`.
+ * @param {string} content - file contents
+ * @param {string} namespace - injected namespace segment (e.g. "ecc")
+ * @returns {string} rewritten contents (unchanged if no matching links)
+ */
+function rewriteNamespaceLinks(content, namespace) {
+  if (typeof content !== 'string' || !namespace) {
+    return content;
+  }
+
+  const pattern = buildLinkPattern();
+  return content.replace(pattern, (match, climb, dir, slash, offset, fullText) => {
+    // Already namespaced (`../../rules/ecc/...`) — leave untouched (idempotent).
+    const rest = fullText.slice(offset + match.length);
+    if (rest.startsWith(`${namespace}/`)) {
+      return match;
+    }
+    return `../${climb}${dir}${slash}${namespace}/`;
+  });
+}
+
+module.exports = { rewriteNamespaceLinks, NAMESPACED_DIRS };

scripts/lib/session-manager.js

@@ -26,6 +26,18 @@ const {
 // "2026-02-01-ChezMoi_2-session.tmp"
 const SESSION_FILENAME_REGEX = /^(\d{4}-\d{2}-\d{2})(?:-([a-zA-Z0-9_][a-zA-Z0-9_-]*))?-session\.tmp$/;
 
+/**
+ * Resolve a file's creation time, preferring birthtime but falling back to
+ * ctime when birthtime is unavailable. Some filesystems (e.g. overlayfs in
+ * containers) report birthtime as epoch 0; a Date object is always truthy, so
+ * `birthtime || ctime` would never fall back. Compare on milliseconds instead.
+ * @param {import('fs').Stats} stats
+ * @returns {Date}
+ */
+function resolveCreatedTime(stats) {
+  return stats.birthtimeMs > 0 ? stats.birthtime : stats.ctime;
+}
+
 /**
  * Parse session filename to extract metadata
  * @param {string} filename - Session filename (e.g., "2026-01-17-abc123-session.tmp" or "2026-01-17-session.tmp")
@@ -116,7 +128,7 @@ function getSessionCandidates(options = {}) {
         hasContent: stats.size > 0,
         size: stats.size,
         modifiedTime: stats.mtime,
-        createdTime: stats.birthtime || stats.ctime
+        createdTime: resolveCreatedTime(stats)
       });
     }
   }
@@ -151,7 +163,7 @@ function buildSessionRecord(sessionPath, metadata) {
     hasContent: stats.size > 0,
     size: stats.size,
     modifiedTime: stats.mtime,
-    createdTime: stats.birthtime || stats.ctime
+    createdTime: resolveCreatedTime(stats)
   };
 }
 

skills/continuous-learning-v2/agents/observer.md

@@ -121,7 +121,7 @@ Validate and sanitize all user input before processing.
 
 When creating instincts, determine scope based on these heuristics:
 
-> **Scope Decision Guide** – See the canonical table in `skills/continuous-learning-v2/SKILL.md` (lines 271‑282).
+> **Scope Decision Guide** – See the canonical table under the "Scope Decision Guide" heading in `skills/continuous-learning-v2/SKILL.md`.
 
 **When in doubt, default to `scope: project`** — it's safer to be project-specific and promote later than to contaminate the global space.
 
@@ -142,7 +142,7 @@ Confidence adjusts over time:
 
 An instinct should be promoted from project-scoped to global when:
 1. The **same pattern** (by id or similar trigger) exists in **2+ different projects**
-2. Each instance has confidence **>= 0.8**
+2. The **average** confidence across those instances is **>= 0.8** (matching `PROMOTE_CONFIDENCE_THRESHOLD` in `instinct-cli.py`)
 3. The domain is in the global-friendly list (security, general-best-practices, workflow)
 
 Promotion is handled by the `instinct-cli.py promote` command or the `/evolve` analysis.

skills/continuous-learning-v2/agents/start-observer.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 # Continuous Learning v2 - Observer Agent Launcher
 #
 # Starts the background observer agent that analyzes observations
@@ -37,7 +37,7 @@ PYTHON_CMD="${CLV2_PYTHON_CMD:-}"
 
 # shellcheck disable=SC1091
 . "${SKILL_ROOT}/scripts/lib/homunculus-dir.sh"
-CONFIG_DIR="$(_ecc_resolve_homunculus_dir)"
+CONFIG_DIR="$(_clv2_resolve_homunculus_dir)"
 if [ -n "${CLV2_CONFIG:-}" ]; then
   CONFIG_FILE="$CLV2_CONFIG"
 elif [ -f "${CONFIG_DIR}/config.json" ]; then
@@ -215,8 +215,13 @@ case "$ACTION" in
       CLV2_OBSERVER_PROMPT_PATTERN="$CLV2_OBSERVER_PROMPT_PATTERN" \
       "$OBSERVER_LOOP_SCRIPT" >> "$LOG_FILE" 2>&1 &
 
-    # Wait for PID file
+    # Wait for the PID file to appear (poll up to ~10s; exits early once ready).
-    sleep 2
+    # A fixed sleep is either too short on loaded/slow filesystems or wastes
+    # time on healthy ones.
+    for _i in $(seq 1 50); do
+      [ -f "$PID_FILE" ] && break
+      sleep 0.2
+    done
 
     # Check for confirmation-seeking output in the observer log
     if tail -n +"$((start_line + 1))" "$LOG_FILE" 2>/dev/null | grep -E -i -q "$CLV2_OBSERVER_PROMPT_PATTERN"; then

skills/continuous-learning-v2/hooks/observe.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 # Continuous Learning v2 - Observation Hook
 #
 # Captures tool use events for pattern analysis.
@@ -135,7 +135,7 @@ fi
 
 # shellcheck disable=SC1091
 . "$(dirname "$0")/../scripts/lib/homunculus-dir.sh"
-CONFIG_DIR="$(_ecc_resolve_homunculus_dir)"
+CONFIG_DIR="$(_clv2_resolve_homunculus_dir)"
 
 # Skip if disabled (check both default and CLV2_CONFIG-derived locations)
 if [ -f "$CONFIG_DIR/disabled" ]; then
@@ -279,11 +279,11 @@ _SECRET_RE = re.compile(
 )
 
 import signal
-def _ecc_bail(*_):
+def _clv2_bail(*_):
     print("[observe] SIGALRM timeout: parse-error fallback observation dropped before write (#2300)", file=sys.stderr)
     sys.exit(0)
 try:
-    signal.signal(signal.SIGALRM, _ecc_bail)
+    signal.signal(signal.SIGALRM, _clv2_bail)
     signal.alarm(8)  # self-terminate before the async hook 10s timeout can orphan us (#2278)
 except Exception:
     pass
@@ -317,11 +317,11 @@ echo "$PARSED" | "$PYTHON_CMD" -c '
 import json, sys, os, re
 import signal
 
-def _ecc_bail(*_):
+def _clv2_bail(*_):
     print("[observe] SIGALRM timeout: in-flight observation dropped before write (#2300)", file=sys.stderr)
     sys.exit(0)
 try:
-    signal.signal(signal.SIGALRM, _ecc_bail)
+    signal.signal(signal.SIGALRM, _clv2_bail)
     signal.alarm(8)  # self-terminate before the async hook 10s timeout can orphan us (#2278)
 except Exception:
     pass
@@ -493,7 +493,7 @@ touch "$ACTIVITY_FILE" 2>/dev/null || true
 # the lazy-start path above. Both wrap the same read-modify-write below.
 should_signal=0
 
-_ecc_bump_signal_counter() {
+_clv2_bump_signal_counter() {
   if [ -f "$SIGNAL_COUNTER_FILE" ]; then
     counter=$(cat "$SIGNAL_COUNTER_FILE" 2>/dev/null || echo 0)
     # Guard against a corrupt counter file: a non-integer value would abort the
@@ -518,7 +518,7 @@ if command -v flock >/dev/null 2>&1 && exec 8>"$SIGNAL_COUNTER_LOCK" 2>/dev/null
   # blocks indefinitely, and only bump the counter while the lock is held -- on
   # a timeout we skip the tick rather than doing an unlocked read-modify-write.
   if flock -w 2 8 2>/dev/null; then
-    _ecc_bump_signal_counter
+    _clv2_bump_signal_counter
     flock -u 8 2>/dev/null || true
   fi
   exec 8>&- 2>/dev/null || true
@@ -547,7 +547,7 @@ else
   done
   if [ "$_signal_lock_held" -eq 1 ]; then
     # Bump only under the held lock -- never an unlocked read-modify-write.
-    _ecc_bump_signal_counter
+    _clv2_bump_signal_counter
     rmdir "$SIGNAL_COUNTER_LOCK" 2>/dev/null || true
     trap - EXIT INT TERM
   fi

skills/continuous-learning-v2/scripts/detect-project.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 # Continuous Learning v2 - Project Detection Helper
 #
 # Shared logic for detecting current project context.
@@ -21,7 +21,7 @@
 
 # shellcheck disable=SC1091
 . "$(dirname "${BASH_SOURCE[0]}")/lib/homunculus-dir.sh"
-_CLV2_HOMUNCULUS_DIR="$(_ecc_resolve_homunculus_dir)"
+_CLV2_HOMUNCULUS_DIR="$(_clv2_resolve_homunculus_dir)"
 _CLV2_PROJECTS_DIR="${_CLV2_HOMUNCULUS_DIR}/projects"
 _CLV2_REGISTRY_FILE="${_CLV2_HOMUNCULUS_DIR}/projects.json"
 

skills/continuous-learning-v2/scripts/lib/homunculus-dir.sh

@@ -6,7 +6,7 @@
 #   2. XDG_DATA_HOME/ecc-homunculus, when XDG_DATA_HOME is absolute
 #   3. HOME/.local/share/ecc-homunculus
 
-_ecc_resolve_homunculus_dir() {
+_clv2_resolve_homunculus_dir() {
   if [ -n "${CLV2_HOMUNCULUS_DIR:-}" ]; then
     case "$CLV2_HOMUNCULUS_DIR" in
       /*) printf '%s\n' "$CLV2_HOMUNCULUS_DIR"; return 0 ;;

skills/continuous-learning-v2/scripts/migrate-homunculus.sh

@@ -7,7 +7,7 @@ OLD="${HOME}/.claude/homunculus"
 
 # shellcheck disable=SC1091
 . "$(dirname "$0")/lib/homunculus-dir.sh"
-NEW="$(_ecc_resolve_homunculus_dir)"
+NEW="$(_clv2_resolve_homunculus_dir)"
 
 if [ "$NEW" = "$OLD" ]; then
   echo "Resolved destination equals source ($OLD); nothing to migrate."

skills/continuous-learning-v2/scripts/test_parse_instinct.py

@@ -19,7 +19,6 @@ import os
 import sys
 from pathlib import Path
 from types import SimpleNamespace
-from unittest import mock
 
 import pytest
 

tests/hooks/observe-signal-counter-race.test.js

@@ -104,7 +104,7 @@ function buildSandbox() {
     path.join(scriptsLibDir, 'homunculus-dir.sh'),
     [
       '#!/bin/bash',
-      '_ecc_resolve_homunculus_dir() { printf "%s\\n" "$HOME/.local/share/ecc-homunculus"; }',
+      '_clv2_resolve_homunculus_dir() { printf "%s\\n" "$HOME/.local/share/ecc-homunculus"; }',
       ''
     ].join('\n')
   );

tests/hooks/observe-signal-timeout.test.js

@@ -3,14 +3,14 @@
  *
  * observe.sh arms a signal.SIGALRM alarm (8s) inside its inline-Python blocks so
  * the observation writer self-terminates before the async hook's 10s timeout can
- * orphan it (#2278). Before #2300 the handler `_ecc_bail` called sys.exit(0) with
+ * orphan it (#2278). Before #2300 the handler `_clv2_bail` called sys.exit(0) with
  * no logging, so a timeout silently dropped the in-flight observation: nothing was
  * logged and the shell saw a clean exit. The fix adds a stderr visibility line to
  * each handler while keeping exit 0 (changing to a non-zero exit would make the
  * Claude hook report a block, per the repo's "always exit 0; log to stderr" rule).
  *
  * Two checks:
- *   1. Static regression guard — every `_ecc_bail` handler in observe.sh writes to
+ *   1. Static regression guard — every `_clv2_bail` handler in observe.sh writes to
  *      sys.stderr before sys.exit(0).
  *   2. Behavioral check — the REAL handler text extracted from observe.sh, when its
  *      alarm fires, exits 0 and emits the `[observe]` visibility token on stderr
@@ -73,14 +73,14 @@ const observeShPath = path.join(
 
 const observeSrc = fs.readFileSync(observeShPath, 'utf8');
 
-// Extract each `_ecc_bail` handler body: the `def` line plus the indented lines
+// Extract each `_clv2_bail` handler body: the `def` line plus the indented lines
 // that follow it, up to (and including) the first dedented `sys.exit(0)` line at
 // the same indentation as the def's body.
 function extractHandlers(src) {
   const lines = src.split('\n');
   const handlers = [];
   for (let i = 0; i < lines.length; i += 1) {
-    if (/^def _ecc_bail\(\*_\):\s*$/.test(lines[i])) {
+    if (/^def _clv2_bail\(\*_\):\s*$/.test(lines[i])) {
       const body = [lines[i]];
       for (let j = i + 1; j < lines.length; j += 1) {
         // Stop when we hit a line that is not indented (next top-level stmt).
@@ -103,15 +103,15 @@ const handlers = extractHandlers(observeSrc);
 // The #2300 timeout handlers are the ones that log the `[observe] SIGALRM
 // timeout` marker. Selecting by marker (rather than by array index) keeps the
 // behavioral check pinned to the timeout handlers even if an unrelated
-// `_ecc_bail` is ever added elsewhere in observe.sh.
+// `_clv2_bail` is ever added elsewhere in observe.sh.
 const timeoutHandlers = handlers.filter(body =>
   body.includes('[observe] SIGALRM timeout')
 );
 
-test('observe.sh defines at least two _ecc_bail timeout handlers', () => {
+test('observe.sh defines at least two _clv2_bail timeout handlers', () => {
   assert.ok(
     handlers.length >= 2,
-    `expected >= 2 _ecc_bail handlers, found ${handlers.length}`
+    `expected >= 2 _clv2_bail handlers, found ${handlers.length}`
   );
   assert.ok(
     timeoutHandlers.length >= 2,
@@ -119,7 +119,7 @@ test('observe.sh defines at least two _ecc_bail timeout handlers', () => {
   );
 });
 
-test('every _ecc_bail handler logs to stderr before exiting (regression guard)', () => {
+test('every _clv2_bail handler logs to stderr before exiting (regression guard)', () => {
   handlers.forEach((body, idx) => {
     const stderrIdx = body.indexOf('file=sys.stderr');
     const exitIdx = body.indexOf('sys.exit(0)');
@@ -142,7 +142,7 @@ test('every _ecc_bail handler logs to stderr before exiting (regression guard)',
   });
 });
 
-test('_ecc_bail handlers keep exit code 0 (no exit 2 / block regression)', () => {
+test('_clv2_bail handlers keep exit code 0 (no exit 2 / block regression)', () => {
   handlers.forEach((body, idx) => {
     assert.ok(
       /sys\.exit\(0\)/.test(body),
@@ -160,7 +160,7 @@ function runHandlerTimeout(python, handler) {
   const program = [
     'import sys, signal, time',
     handler,
-    'signal.signal(signal.SIGALRM, _ecc_bail)',
+    'signal.signal(signal.SIGALRM, _clv2_bail)',
     'signal.alarm(1)',
     'time.sleep(3)',
     'print("REACHED_END_SHOULD_NOT_HAPPEN")',
@@ -178,7 +178,7 @@ function runHandlerTimeout(python, handler) {
 // the worst case. A behavioral check on only one handler would not catch a
 // regression that silenced another.
 timeoutHandlers.forEach((handler, idx) => {
-  test(`real _ecc_bail timeout handler #${idx + 1}: SIGALRM fire emits stderr token and exits 0`, () => {
+  test(`real _clv2_bail timeout handler #${idx + 1}: SIGALRM fire emits stderr token and exits 0`, () => {
     const python = findPython();
     if (!python) {
       // Fail fast rather than returning (which the harness would record as a

tests/hooks/observer-memory.test.js

@@ -375,7 +375,7 @@ test('observe.sh creates counter file and increments on each call', () => {
     path.join(scriptsLibDir, 'homunculus-dir.sh'),
     [
       '#!/bin/bash',
-      '_ecc_resolve_homunculus_dir() { printf "%s\\n" "$HOME/.local/share/ecc-homunculus"; }',
+      '_clv2_resolve_homunculus_dir() { printf "%s\\n" "$HOME/.local/share/ecc-homunculus"; }',
       ''
     ].join('\n')
   );

tests/lib/rewrite-namespace-links.test.js

@@ -0,0 +1,81 @@
+/**
+ * Tests for scripts/lib/install/rewrite-namespace-links.js (#2340)
+ */
+
+const assert = require('assert');
+
+const { rewriteNamespaceLinks } = require('../../scripts/lib/install/rewrite-namespace-links');
+
+function test(name, fn) {
+  try {
+    fn();
+    console.log(`  \u2713 ${name}`);
+    return true;
+  } catch (error) {
+    console.log(`  \u2717 ${name}`);
+    console.log(`    Error: ${error.message}`);
+    return false;
+  }
+}
+
+function runTests() {
+  console.log('\n=== Testing rewrite-namespace-links.js ===\n');
+
+  let passed = 0;
+  let failed = 0;
+
+  if (test('rewrites a markdown link to a sibling rules dir', () => {
+    assert.strictEqual(
+      rewriteNamespaceLinks('See [hooks](../../rules/react/hooks.md) here', 'ecc'),
+      'See [hooks](../../../rules/ecc/react/hooks.md) here'
+    );
+  })) passed++; else failed++;
+
+  if (test('rewrites a bare rules dir link', () => {
+    assert.strictEqual(
+      rewriteNamespaceLinks('Rules: [r](../../rules/react/)', 'ecc'),
+      'Rules: [r](../../../rules/ecc/react/)'
+    );
+  })) passed++; else failed++;
+
+  if (test('handles deeper skill nesting (3+ climbs)', () => {
+    assert.strictEqual(
+      rewriteNamespaceLinks('link ../../../rules/x/y.md', 'ecc'),
+      'link ../../../../rules/ecc/x/y.md'
+    );
+  })) passed++; else failed++;
+
+  if (test('leaves intra-skill single-climb links untouched', () => {
+    const input = 'See ../sibling/file.md and ./local.md';
+    assert.strictEqual(rewriteNamespaceLinks(input, 'ecc'), input);
+  })) passed++; else failed++;
+
+  if (test('is idempotent on already-namespaced links', () => {
+    const input = 'See [x](../../../rules/ecc/react/hooks.md)';
+    assert.strictEqual(rewriteNamespaceLinks(input, 'ecc'), input);
+  })) passed++; else failed++;
+
+  if (test('rewrites multiple links in one document', () => {
+    assert.strictEqual(
+      rewriteNamespaceLinks('(../../rules/a) and (../../rules/b)', 'ecc'),
+      '(../../../rules/ecc/a) and (../../../rules/ecc/b)'
+    );
+  })) passed++; else failed++;
+
+  if (test('rewrites sibling skills-dir links symmetrically', () => {
+    assert.strictEqual(
+      rewriteNamespaceLinks('[s](../../skills/other/SKILL.md)', 'ecc'),
+      '[s](../../../skills/ecc/other/SKILL.md)'
+    );
+  })) passed++; else failed++;
+
+  if (test('returns input unchanged when namespace is missing', () => {
+    const input = 'See [x](../../rules/react/)';
+    assert.strictEqual(rewriteNamespaceLinks(input, ''), input);
+  })) passed++; else failed++;
+
+  console.log(`\nResults: Passed: ${passed}, Failed: ${failed}`);
+  process.exit(failed > 0 ? 1 : 0);
+}
+
+runTests();

tests/lib/session-manager.test.js

@@ -1165,16 +1165,21 @@ src/main.ts
   })) passed++; else failed++;
 
   if (test('createdTime falls back to ctime when birthtime is epoch-zero', () => {
-    // This tests the || fallback logic: stats.birthtime || stats.ctime
+    // Some filesystems (e.g. overlayfs in containers) report birthtime as
-    // On some FS, birthtime may be epoch 0 (falsy as a Date number comparison
+    // epoch 0. A Date object is always truthy, so `birthtime || ctime` would
-    // but truthy as a Date object). The fallback is defensive.
+    // never fall back; the source compares birthtimeMs > 0 instead. Verify the
+    // resolved createdTime is always a non-zero Date regardless of birthtime.
     const stats = fs.statSync(r33FilePath);
-    // Both birthtime and ctime should be valid Dates on any modern OS
     assert.ok(stats.ctime instanceof Date, 'ctime should exist');
-    // The fallback expression `birthtime || ctime` should always produce a valid Date
+    const expected = stats.birthtimeMs > 0 ? stats.birthtime : stats.ctime;
-    const fallbackResult = stats.birthtime || stats.ctime;
+    assert.ok(expected.getTime() > 0, 'Resolved created time should be non-zero');
-    assert.ok(fallbackResult instanceof Date, 'Fallback should produce a Date');
+    const session = sessionManager.getSessionById('r33birth');
-    assert.ok(fallbackResult.getTime() > 0, 'Fallback date should be non-zero');
+    assert.ok(session, 'Should find the session');
+    assert.strictEqual(
+      session.createdTime.getTime(),
+      expected.getTime(),
+      'createdTime should fall back to ctime when birthtime is epoch-zero'
+    );
   })) passed++; else failed++;
 
   // Cleanup Round 33 HOME override

tests/scripts/install-apply.test.js

@@ -123,6 +123,40 @@ function runTests() {
     }
   })) passed++; else failed++;
 
+  if (test('rewrites namespaced skill links to the ecc/ rules path (#2340)', () => {
+    const homeDir = createTempDir('install-apply-home-');
+    const projectDir = createTempDir('install-apply-project-');
+
+    try {
+      const result = run(['typescript'], { cwd: projectDir, homeDir });
+      assert.strictEqual(result.code, 0, result.stderr);
+
+      const claudeRoot = path.join(homeDir, '.claude');
+      const skillPath = path.join(claudeRoot, 'skills', 'ecc', 'react-patterns', 'SKILL.md');
+      assert.ok(fs.existsSync(skillPath), 'react-patterns SKILL.md should be installed');
+
+      const content = fs.readFileSync(skillPath, 'utf8');
+      assert.ok(
+        content.includes('../../../rules/ecc/react/'),
+        'source-relative rules link should be rewritten for the ecc/ namespace'
+      );
+      assert.ok(
+        !content.includes('](../../rules/'),
+        'no un-namespaced ](../../rules/ links should remain'
+      );
+
+      // The rewritten link must resolve to a file that actually exists on disk.
+      const linkTarget = path.join(
+        path.dirname(skillPath),
+        '../../../rules/ecc/react/hooks.md'
+      );
+      assert.ok(fs.existsSync(linkTarget), 'rewritten link target should exist');
+    } finally {
+      cleanup(homeDir);
+      cleanup(projectDir);
+    }
+  })) passed++; else failed++;
+
   if (test('installs Cursor configs and writes install-state', () => {
     const homeDir = createTempDir('install-apply-home-');
     const projectDir = createTempDir('install-apply-project-');