feat(deploy): install update/remove scripts into .mam_deploy/ and refine markdown staging

deploy/install_mam.sh

@@ -114,15 +114,27 @@ log_info "Deploying orchestration rules & skills (.agents/)..."
 mkdir -p "$TARGET_DIR/.agents"
  
 # Sync rules and skills, avoiding copying temporary or system files
-# Exclude git histories, reports, logs or internal runtime cache if any
-rsync -a --exclude='.git/' --exclude='/reports/' --exclude='*.log' --exclude='__pycache__/' --exclude='*.pyc' "$SRC_DIR/.agents/" "$TARGET_DIR/.agents/"
+# Exclude git histories, reports, references, logs or internal runtime cache
+rsync -a --exclude='.git/' --exclude='/reports/' --exclude='/references/' --exclude='*.log' --exclude='*.tmp' --exclude='__pycache__/' --exclude='*.pyc' "$SRC_DIR/.agents/" "$TARGET_DIR/.agents/"
 log_ok "Deployed Rules and Skills under target's .agents/"
- 
+
 # Copy config templates and generate scripts (M-2)
 if [ -f "$SRC_DIR/.mam.env.example" ]; then
   cp "$SRC_DIR/.mam.env.example" "$TARGET_DIR/.mam.env.example"
   log_ok "Copied .mam.env.example configuration template"
 fi
+
+# Deploy remove.sh and update.sh into .mam_deploy/ (R-3)
+mkdir -p "$TARGET_DIR/.mam_deploy"
+if [ -f "$SRC_DIR/deploy/remove.sh" ]; then
+  cp "$SRC_DIR/deploy/remove.sh" "$TARGET_DIR/.mam_deploy/remove.sh"
+  chmod 0755 "$TARGET_DIR/.mam_deploy/remove.sh"
+fi
+if [ -f "$SRC_DIR/deploy/update.sh" ]; then
+  cp "$SRC_DIR/deploy/update.sh" "$TARGET_DIR/.mam_deploy/update.sh"
+  chmod 0755 "$TARGET_DIR/.mam_deploy/update.sh"
+fi
+
 if [ -f "$SRC_DIR/deploy/generate-env.sh" ]; then
   mkdir -p "$TARGET_DIR/scripts"
   cp "$SRC_DIR/deploy/generate-env.sh" "$TARGET_DIR/scripts/generate-env.sh"
@@ -160,32 +172,62 @@ else
   log_ok "Guidelines AGENTS.md copied to project root."
 fi
 
-# 4. Gitignore adjustments
+# 4. Gitignore adjustments (R-4: managed block)
 log_info "Registering runtime isolation blocks in .gitignore..."
 GITIGNORE="$TARGET_DIR/.gitignore"
-MAM_PATTERN="/.mam/"
-VENV_PATTERN="/.venv/"
- 
-if [ -f "$GITIGNORE" ]; then
-  # Register .mam/ if absent
-  if grep -Eq '^/?\.mam/?$' "$GITIGNORE"; then
-    log_ok ".mam/ already registered in target's .gitignore."
-  else
-    echo -e "\n# Multi-Agent Mux (MAM) runtime databases and isolation cache\n$MAM_PATTERN" >> "$GITIGNORE"
-    log_ok "Appended /.mam/ registration to .gitignore."
-  fi
- 
-  # Register .venv/ if absent
-  if grep -Eq '^/?\.venv/?$' "$GITIGNORE"; then
-    log_ok ".venv/ already registered in target's .gitignore."
-  else
-    echo -e "\n# Python virtual environment\n$VENV_PATTERN" >> "$GITIGNORE"
-    log_ok "Appended /.venv/ registration to .gitignore."
-  fi
-else
-  echo -e "# Multi-Agent Mux (MAM) runtime databases and isolation cache\n$MAM_PATTERN\n\n# Python virtual environment\n$VENV_PATTERN" > "$GITIGNORE"
-  log_ok "Created .gitignore with MAM and .venv exclusions."
-fi
+MAM_GI_START="# >>> MAM managed block (managed by install.sh — do not edit) >>>"
+MAM_GI_END="# <<< MAM managed block <<<"
+
+python3 - "$GITIGNORE" "$MAM_GI_START" "$MAM_GI_END" <<'PY'
+import sys, os
+
+gi_path, start_marker, end_marker = sys.argv[1], sys.argv[2], sys.argv[3]
+
+block_lines = [
+    start_marker + "\n",
+    "/.venv/\n",
+    "/.mam/\n",
+    "/.mam_deploy/\n",
+    "/.mam.env\n",
+    "/.mam.env.*\n",
+    "!/.mam.env.example\n",
+    "/.cache/multi-agent-mux-monitor/\n",
+    "/.mam-skill-backup.*/\n",
+    "CURRENT_JOB.md\n",
+    end_marker + "\n"
+]
+
+lines = []
+if os.path.exists(gi_path):
+    with open(gi_path, "r") as f:
+        lines = f.readlines()
+
+new_lines = []
+in_block = False
+block_inserted = False
+
+for line in lines:
+    if line.strip() == start_marker:
+        in_block = True
+        if not block_inserted:
+            new_lines.extend(block_lines)
+            block_inserted = True
+        continue
+    if line.strip() == end_marker:
+        in_block = False
+        continue
+    if not in_block:
+        new_lines.append(line)
+
+if not block_inserted:
+    if new_lines and not new_lines[-1].endswith("\n"):
+        new_lines[-1] += "\n"
+    new_lines.extend(block_lines)
+
+with open(gi_path, "w") as f:
+    f.writelines(new_lines)
+PY
+log_ok "Registered MAM managed block in .gitignore."
 
 # 5. Python Virtual Environment Setup (F-1)
 log_info "Bootstrapping Python virtual environment (.venv) in target..."