Refresh configs, add update.fish, rewrite README as setup runbook

- Re-dump brewfile (adds postgresql@16, tree; drops typeit4me)
- Refresh claude-settings.json, hosts, and serena_config.yml from machine
- Add update.fish to actualise the copied configs in one go
- Rewrite README as a complete ordered fresh-machine setup guide

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01MN5eka2MuNJP9uCMdTda75

update.fish

@@ -0,0 +1,58 @@
+#!/usr/bin/env fish
+
+# Actualise the tracked config files from the current machine state.
+#
+# Most files in this repo are symlinked into place (see README), so they are
+# always current. This script refreshes the ones that are plain copies and
+# therefore drift out of date:
+#
+#   * brewfile             <- `brew bundle dump`
+#   * claude-settings.json <- ~/.claude/settings.json
+#   * hosts                <- /etc/hosts
+#   * serena_config.yml    <- ~/.serena/serena_config.yml
+#
+# Safe to re-run. Review the diff afterwards and commit what you want to keep.
+
+set -l repo (dirname (status --current-filename))
+cd $repo; or exit 1
+
+echo "Actualising config in $repo"
+echo
+
+# --- Homebrew packages, casks and VS Code extensions -----------------------
+if type -q brew
+    echo "==> Dumping Homebrew bundle -> brewfile"
+    brew bundle dump --file=brewfile --force
+else
+    echo "==> Skipping brewfile (brew not found)"
+end
+
+# --- Claude Code settings --------------------------------------------------
+set -l claude_settings "$HOME/.claude/settings.json"
+if test -f $claude_settings
+    echo "==> Copying $claude_settings -> claude-settings.json"
+    cp $claude_settings claude-settings.json
+else
+    echo "==> Skipping claude-settings.json ($claude_settings not found)"
+end
+
+# --- Serena config ---------------------------------------------------------
+set -l serena_config "$HOME/.serena/serena_config.yml"
+if test -f $serena_config
+    echo "==> Copying $serena_config -> serena_config.yml"
+    cp $serena_config serena_config.yml
+else
+    echo "==> Skipping serena_config.yml ($serena_config not found)"
+end
+
+# --- /etc/hosts ------------------------------------------------------------
+if test -f /etc/hosts
+    echo "==> Copying /etc/hosts -> hosts"
+    cp /etc/hosts hosts
+else
+    echo "==> Skipping hosts (/etc/hosts not found)"
+end
+
+echo
+echo "Done. Review changes:"
+echo "    git -C $repo diff --stat"