From f86a8560ebaf7b1eecf61e60207bb5d96b8efe33 Mon Sep 17 00:00:00 2001
From: gnekt <dima9610@gmail.com>
Date: Mon, 23 Mar 2026 22:39:33 +0100
Subject: [PATCH] Add core-manifest for references to protect user-created
 reference docs

Same pattern as agents: launchme/updateme write a .core-manifest in
.claude/references/ listing installed core files. The deprecation loop
only touches files in the manifest, leaving user-created references
untouched.
---
 scripts/launchme.sh |  6 +++++-
 scripts/updateme.sh | 33 +++++++++++++++++++++------------
 2 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/scripts/launchme.sh b/scripts/launchme.sh
index d7d7e1a..b977da7 100755
--- a/scripts/launchme.sh
+++ b/scripts/launchme.sh
@@ -120,7 +120,11 @@ success "Copied $AGENT_COUNT agents"
 # ── Copy references ─────────────────────────────────────────────────────────
 info "Creating .claude/references/ in vault..."
 mkdir -p "$VAULT_DIR/.claude/references"
-cp "$REPO_DIR/references/"*.md "$VAULT_DIR/.claude/references/"
+: > "$VAULT_DIR/.claude/references/.core-manifest"
+for ref in "$REPO_DIR/references/"*.md; do
+  cp "$ref" "$VAULT_DIR/.claude/references/"
+  basename "$ref" >> "$VAULT_DIR/.claude/references/.core-manifest"
+done
 success "Copied references"
 
 # ── Generate and copy skills (for Cowork/Desktop) ───────────────────────────
diff --git a/scripts/updateme.sh b/scripts/updateme.sh
index bf56d67..87f4f0b 100755
--- a/scripts/updateme.sh
+++ b/scripts/updateme.sh
@@ -113,25 +113,20 @@ for agent in "$REPO_DIR/agents/"*.md; do
   fi
 done
 
-# ── Update references ───────────────────────────────────────────────────────
-REF_COUNT=0
-mkdir -p "$VAULT_DIR/.claude/references"
-for ref in "$REPO_DIR/references/"*.md; do
-  name="$(basename "$ref")"
-  if ! diff -q "$ref" "$VAULT_DIR/.claude/references/$name" >/dev/null 2>&1; then
-    cp "$ref" "$VAULT_DIR/.claude/references/"
-    info "Updated reference: $name"
-    REF_COUNT=$((REF_COUNT + 1))
-  fi
-done
-
 # ── Deprecate removed references ──────────────────────────────────────────
+# Read the old manifest before rewriting, same logic as agents.
+REF_MANIFEST="$VAULT_DIR/.claude/references/.core-manifest"
 for vault_ref in "$VAULT_DIR/.claude/references/"*.md; do
   [[ -f "$vault_ref" ]] || continue
   name="$(basename "$vault_ref")"
   [[ -f "$REPO_DIR/references/$name" ]] && continue
   [[ "$name" == *"-DEPRECATED"* ]] && continue
+  # Skip user-created references: only deprecate if listed in the manifest
+  if [[ -f "$REF_MANIFEST" ]] && ! grep -qxF "$name" "$REF_MANIFEST"; then
+    continue
+  fi
   deprecated_name="${name%.md}-DEPRECATED.md"
+  [[ -f "$VAULT_DIR/.claude/references/$deprecated_name" ]] && continue
   mv "$vault_ref" "$VAULT_DIR/.claude/references/$deprecated_name"
   { echo "########"; echo "DEPRECATED DO NOT USE"; echo "########"; echo ""; cat "$VAULT_DIR/.claude/references/$deprecated_name"; } > "$VAULT_DIR/.claude/references/$deprecated_name.tmp"
   mv "$VAULT_DIR/.claude/references/$deprecated_name.tmp" "$VAULT_DIR/.claude/references/$deprecated_name"
@@ -139,6 +134,20 @@ for vault_ref in "$VAULT_DIR/.claude/references/"*.md; do
   DEPRECATED_COUNT=$((DEPRECATED_COUNT + 1))
 done
 
+# ── Update references and rewrite manifest ────────────────────────────────
+REF_COUNT=0
+mkdir -p "$VAULT_DIR/.claude/references"
+: > "$VAULT_DIR/.claude/references/.core-manifest"
+for ref in "$REPO_DIR/references/"*.md; do
+  name="$(basename "$ref")"
+  basename "$ref" >> "$VAULT_DIR/.claude/references/.core-manifest"
+  if ! diff -q "$ref" "$VAULT_DIR/.claude/references/$name" >/dev/null 2>&1; then
+    cp "$ref" "$VAULT_DIR/.claude/references/"
+    info "Updated reference: $name"
+    REF_COUNT=$((REF_COUNT + 1))
+  fi
+done
+
 # ── Regenerate and update skills ───────────────────────────────────────────
 SKILL_COUNT=0
 if command -v python3 >/dev/null 2>&1 && [[ -f "$REPO_DIR/scripts/generate-skills.py" ]]; then