fix: resolve open-issue cluster (#2295, #2298, #2303–#2306, #2340) + createdTime fallback bug (#2408)

* fix: resolve issue cluster (#2295,#2298,#2303,#2304,#2305,#2306,#2340) + createdTime fallback bug

- session-manager: fix createdTime birthtime||ctime fallback that never fired
  (a Date is always truthy); use birthtimeMs>0 check via resolveCreatedTime()
- installer: rewrite source-relative rules/skills links for the injected
  ecc/ namespace so installed skills resolve correctly (#2340)
- continuous-learning-v2: drop unused mock import (#2305); standardize bash
  shebangs (#2303); poll for PID file instead of fixed sleep (#2295);
  rename _ecc_* -> _clv2_* (#2304); align promotion confidence docs (#2298);
  de-brittle Scope Decision Guide cross-reference (#2306)

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

* fix(ci): resync lockfiles with package.json (eslint 10) + migrate yarn.lock to Yarn 4 format

package.json requires eslint@^10.6.0 but the committed locks pinned 9.39.2, so
npm ci aborted and Yarn 4 hardened mode rejected the stale v1-classic yarn.lock
(YN0028). Regenerate package-lock.json and rewrite yarn.lock in Yarn 4 (berry)
format so npm ci and immutable yarn installs both pass.

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

* 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>

* fix(observer): portable mktemp template on BSD/macOS (#2417); correct false attribution-disabled claim in git-workflow docs (#2426) (#2430)

Co-authored-by: affaan <affaan@itomarkets.com>
Co-authored-by: Devin AI <158243242+devin-ai-integration[bot]@users.noreply.github.com>

* fix: remove duplicate resolveCreatedTime introduced by merge (no-redeclare)

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

* fix: restore heading-based Scope Decision Guide ref (line numbers drift) + keep behavioral #2340 install test

---------

Co-authored-by: affaan <affaan@itomarkets.com>
Co-authored-by: Devin AI <158243242+devin-ai-integration[bot]@users.noreply.github.com>
Co-authored-by: Affaan Mustafa <me@affaanmustafa.com>

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

@@ -145,7 +145,10 @@ analyze_observations() {
   MAX_ANALYSIS_LINES="${ECC_OBSERVER_MAX_ANALYSIS_LINES:-500}"
   observer_tmp_dir="${PROJECT_DIR}/.observer-tmp"
   mkdir -p "$observer_tmp_dir"
-  analysis_file="$(mktemp "${observer_tmp_dir}/ecc-observer-analysis.XXXXXX.jsonl")"
+  # Keep the XXXXXX run at the very end of the template: BSD/macOS mktemp only
+  # substitutes a trailing X run, so a suffix after it (e.g. `.jsonl`) produces a
+  # literal, non-random name that wedges every later cycle with "File exists" (#2417).
+  analysis_file="$(mktemp "${observer_tmp_dir}/ecc-observer-analysis.jsonl.XXXXXX")"
   tail -n "$MAX_ANALYSIS_LINES" "$OBSERVATIONS_FILE" > "$analysis_file"
   analysis_count=$(wc -l < "$analysis_file" 2>/dev/null || echo 0)
   echo "[$(date)] Using last $analysis_count of $obs_count observations for analysis" >> "$LOG_FILE"

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.
 

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

@@ -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

@@ -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