feat: multi-agent-mux-update skill and in-place install (Issue #72)

The update is a skill (decision 4); deploy/update.sh and the installed
.mam_deploy/update.sh are gone.

- Phase 1 (installed code, update.sh): publish the update marker under the
  exclusive admission lock; refuse before any change while a running row, a
  live herdr agent in the workspace on any running server, an open job
  (unreadable JSON included, dry_run not), a live loop marker or a
  monitor.lock held by a monitor the skills did not start (U3) is there - the
  calling agent (server + pane, its row and one running job) excepted
  (lib_py/update.py precheck, decisions 1 and 7). Stop the monitor (TERM, then
  KILL and restart it if it does not end; decision 2), handle a leftover
  backup by its state (U4), back up .agents, .mam_deploy, root files, .venv,
  the installer's .mam files and the registry (SQLite backup API under the
  registry lock) into .mam/update-backup/, then exec a copy of
  install_phase.sh outside the tree (decision 5).
- The copy (no lib.sh/lib_py, bash 3.2) runs the installer in place; on
  failure it restores the backup and restarts the monitor from the restored
  tree; on success it runs phase 2, post_update.sh of the new tree, which
  converts the registry with lib_py.registry_format and restarts the monitor
  if it ran. The backup and the marker are removed at the end.
- install.sh updates in place (decisions 3, 4, 9): install_state keys are set,
  one line each; no updater is installed and an old one (.mam_deploy/update.sh,
  or a root update.sh the manifest lists) is removed; framework files the new
  version no longer ships are deleted when unmodified, kept and listed when
  modified, and dropped from base/, the manifest and asset_hashes.txt; a local
  source's .mam is not staged. remove.sh knows the new skill; CI shellchecks
  its scripts; docs point at the skill.
- test_issue8_update_state and test_deploy_layout td6/td27 run the skill.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

deploy/install.sh

@@ -125,7 +125,9 @@ if [ "$REFRESH" -eq 1 ] || [ "${MAM_SKIP_VENV:-0}" -eq 1 ] || ! check_assets_pre
   FETCH_METHOD="archive"
   if [ -d "$REPO_URL" ]; then
     echo "🌐 Copying local working tree into a staging area..."
-    cp -R "$REPO_URL/." "$STAGE_DIR/"
+    # Everything but .mam/: runtime state is never staged, and it may hold the
+    # update skill's rollback copy (.mam/update-backup/, Issue #72).
+    find "$REPO_URL/." -mindepth 1 -maxdepth 1 ! -name .mam -exec cp -R {} "$STAGE_DIR/" \;
     FETCH_METHOD="local"
   elif command -v git &>/dev/null; then
     echo "🌐 Cloning repository (shallow) into a staging area..."
@@ -157,9 +159,15 @@ if [ "$REFRESH" -eq 1 ] || [ "${MAM_SKIP_VENV:-0}" -eq 1 ] || ! check_assets_pre
   MANIFEST_FILE=".mam/install_manifest.txt"
   touch "$MANIFEST_FILE"
 
-  # Migrate legacy root layout for remove.sh and update.sh into .mam_deploy/ if owned
+  # Drop every line naming this path from the manifest
+  manifest_drop() {
+    grep -Fvx -- "$1" "$MANIFEST_FILE" > "$MANIFEST_FILE.tmp" || true
+    mv -f "$MANIFEST_FILE.tmp" "$MANIFEST_FILE"
+  }
+
+  # Migrate legacy root layout for remove.sh into .mam_deploy/ if owned
   mkdir -p .mam_deploy
-  for legacy_script in remove.sh update.sh; do
+  for legacy_script in remove.sh; do
     if [ -f "$legacy_script" ] && grep -Fqx "$legacy_script" "$MANIFEST_FILE" 2>/dev/null; then
       mv -f "$legacy_script" ".mam_deploy/$legacy_script"
       python3 -c '
@@ -179,6 +187,13 @@ with open(path, "w") as f:
     fi
   done
 
+  # update.sh is no longer shipped (Issue #72; the multi-agent-mux-update skill
+  # updates). A legacy root update.sh goes only if the manifest says we put it there.
+  if [ -f update.sh ] && grep -Fqx update.sh "$MANIFEST_FILE" 2>/dev/null; then
+    rm -f update.sh
+    manifest_drop update.sh
+  fi
+
   # Safe refresh & fingerprint checking logic
   TS=$(date -u +%Y%m%dT%H%M%SZ)
   FRAMEWORK_LEDGER=".mam/.framework_ledger.tmp"
@@ -374,7 +389,7 @@ MERGEREG
     fi
   done
 
-  # Install remove.sh and update.sh into .mam_deploy/
+  # Install remove.sh into .mam_deploy/
   mkdir -p .mam_deploy
   if [ -f "$STAGE_DIR/deploy/remove.sh" ]; then
     cp "$STAGE_DIR/deploy/remove.sh" .mam_deploy/remove.sh
@@ -384,13 +399,9 @@ MERGEREG
     fi
   fi
 
-  if [ -f "$STAGE_DIR/deploy/update.sh" ]; then
-    cp "$STAGE_DIR/deploy/update.sh" .mam_deploy/update.sh
-    chmod 0755 .mam_deploy/update.sh
-    if ! grep -Fqx ".mam_deploy/update.sh" "$MANIFEST_FILE" 2>/dev/null; then
-      echo ".mam_deploy/update.sh" >> "$MANIFEST_FILE"
-    fi
-  fi
+  # An older install's updater is not shipped any more (Issue #72)
+  rm -f .mam_deploy/update.sh
+  manifest_drop .mam_deploy/update.sh
 
   if [ -f "$STAGE_DIR/.mam.env.example" ] && [ ! -e ".mam.env.example" ]; then
     cp "$STAGE_DIR/.mam.env.example" .
@@ -407,6 +418,34 @@ MERGEREG
     fi
   fi
 
+  # Framework-owned files the previous install recorded (manifest and
+  # asset_hashes.txt) that this version no longer ships (Issue #72). Unmodified
+  # ones are deleted. Modified ones are kept and become the user's file: they
+  # leave the manifest, so remove.sh leaves them alone, and asset_hashes.txt
+  # (rebuilt below from the shipped files only).
+  if [ -f .mam/asset_hashes.txt ]; then
+    SHIPPED_LIST=".mam/.shipped_paths.tmp"
+    cut -f2 "$FRAMEWORK_LEDGER" > "$SHIPPED_LIST"
+    while read -r _old_sha _old_path; do
+      [ -n "${_old_path:-}" ] || continue
+      is_framework_owned "$_old_path" || continue
+      grep -Fqx -- "$_old_path" "$MANIFEST_FILE" || continue
+      if grep -Fqx -- "$_old_path" "$SHIPPED_LIST"; then continue; fi
+      if [ -f "$_old_path" ] && [ "$(python3 -c 'import hashlib, sys; print(hashlib.sha256(open(sys.argv[1], "rb").read()).hexdigest())' "$_old_path")" != "$_old_sha" ]; then
+        echo "ℹ️  Local modification detected (no longer shipped, kept as yours): $_old_path" >&2
+      else
+        rm -f "$_old_path"
+        _old_dir="$(dirname "$_old_path")"
+        while [ "$_old_dir" != ".agents" ] && rmdir "$_old_dir" 2>/dev/null; do
+          _old_dir="$(dirname "$_old_dir")"
+        done
+      fi
+      rm -f ".mam/base/$_old_path"
+      manifest_drop "$_old_path"
+    done < .mam/asset_hashes.txt
+    rm -f "$SHIPPED_LIST"
+  fi
+
   # Re-build asset_hashes.txt from the UPSTREAM copy of every framework-owned file
   python3 - .mam/asset_hashes.txt "$FRAMEWORK_LEDGER" <<'HASHDB'
 import os, hashlib, sys
@@ -590,15 +629,25 @@ with open(gi_path, "w") as f:
 PY
 
 if [ "${MAM_SKIP_GITIGNORE:-0}" -eq 0 ]; then
+  # Set the key: overwrite it in place, one line per key, other keys kept
   python3 -c '
 import os
+os.makedirs(".mam", exist_ok=True)
+lines = []
 if os.path.exists(".mam/install_state"):
-    with open(".mam/install_state", "a") as f:
-        f.write("gitignore_created=1\n")
-else:
-    os.makedirs(".mam", exist_ok=True)
-    with open(".mam/install_state", "w") as f:
-        f.write("gitignore_created=1\n")
+    with open(".mam/install_state") as f:
+        lines = f.read().splitlines()
+out, done = [], False
+for line in lines:
+    if line.startswith("gitignore_created="):
+        if done:
+            continue
+        line, done = "gitignore_created=1", True
+    out.append(line)
+if not done:
+    out.append("gitignore_created=1")
+with open(".mam/install_state", "w") as f:
+    f.write("\n".join(out) + "\n")
 '
 fi
 
@@ -617,6 +666,6 @@ cat <<EOF
      $ bash .agents/skills/multi-agent-mux-status/scripts/status.sh
 
   3. Update installed skills in the future:
-     $ bash .mam_deploy/update.sh
+     $ bash .agents/skills/multi-agent-mux-update/scripts/update.sh
 --------------------------------------------------------------------------------
 EOF