fix: warn when populated legacy ~/.claude/homunculus exists (#2036)

After the XDG migration the CLI reads from
$XDG_DATA_HOME/ecc-homunculus/ (default ~/.local/share/ecc-homunculus/),
but installs that retained an older manual copy at ~/.claude/homunculus/
saw observations land in the new location while `instinct-cli.py status`
silently continued to look at the new directory only. The reporter
spent hours tracing the divergence because nothing surfaced the legacy
tree.

Add `_detect_legacy_homunculus_dir()` which returns the legacy path
when ~/.claude/homunculus/ contains real ECC state (projects/,
instincts/, evolved/, or observations.jsonl) and the active
HOMUNCULUS_DIR is different. `cmd_status` calls it at the bottom of
its output and prints a one-time, scoped warning that names both
paths and points at the existing migrate-homunculus.sh script.

Empty placeholder directories (just ~/.claude/homunculus/ with no
content) are ignored so users who have already migrated and left the
empty shell behind don't get nagged on every status call.

Tests cover three branches: populated legacy dir triggers the warning,
absent legacy dir stays silent, and empty placeholder legacy dir stays
silent.

skills/continuous-learning-v2/scripts/instinct-cli.py

@@ -67,6 +67,35 @@ def _ensure_global_dirs():
         d.mkdir(parents=True, exist_ok=True)
 
 
+def _detect_legacy_homunculus_dir() -> "Path | None":
+    """Detect a populated legacy ~/.claude/homunculus tree that the current
+    XDG-based CLI does NOT read from.
+
+    Issue #2036: when ECC migrated to XDG_DATA_HOME (default
+    ~/.local/share/ecc-homunculus/), users with an older manual install at
+    ~/.claude/homunculus/ silently had observations written to the new path
+    while `instinct-cli.py status` continued to look at the old one. We warn
+    explicitly when both paths exist so the divergence is visible instead of
+    appearing as "system is broken".
+    """
+    legacy = Path.home() / ".claude" / "homunculus"
+    if legacy == HOMUNCULUS_DIR:
+        return None
+    try:
+        if not legacy.is_dir():
+            return None
+        # Treat the directory as populated only if it contains real ECC
+        # state -- projects/, instincts/, evolved/, or observations.jsonl.
+        # An empty placeholder dir is not worth warning about.
+        for marker in ("projects", "instincts", "evolved", "observations.jsonl"):
+            target = legacy / marker
+            if target.exists():
+                return legacy
+    except OSError:
+        return None
+    return None
+
+
 # ─────────────────────────────────────────────
 # Path Validation
 # ─────────────────────────────────────────────
@@ -460,6 +489,24 @@ def cmd_status(args) -> int:
                 days_left = max(0, PENDING_TTL_DAYS - item["age_days"])
                 print(f"    - {item['name']} ({days_left}d remaining)")
 
+    # Issue #2036: legacy ~/.claude/homunculus is invisible to the current
+    # XDG-based CLI. Surface the divergence so users debugging "no instincts
+    # found" don't spend hours tracing path mismatches.
+    legacy_dir = _detect_legacy_homunculus_dir()
+    if legacy_dir is not None:
+        migrate_script = (
+            Path(__file__).resolve().parent / "migrate-homunculus.sh"
+        )
+        print(f"\n{'-'*60}")
+        print(f"  WARNING: Legacy data found at {legacy_dir}")
+        print(f"    The current CLI reads from {HOMUNCULUS_DIR}")
+        print( "    and does NOT see anything under the legacy path.")
+        if migrate_script.exists():
+            print(f"    Run: {migrate_script}")
+        else:
+            print(f"    Migrate by moving {legacy_dir} into {HOMUNCULUS_DIR}")
+        print( "    (or remove the legacy directory once you've confirmed it's empty).")
+
     print(f"\n{'='*60}\n")
     return 0