fix: ground + fix three Pillar-9 candidate bugs from the script sweep

All three confirmed real on inspection.

1. nomarchy-refresh-config was dead on every system: it read
   /etc/nixos/nomarchy/{core/home/config,features} (the source tree never
   lands there — only /etc/nomarchy on VM-guest/live ISO) and fell back to
   ~/.local/share/nomarchy/config, which nothing deployed despite SKILL.md
   documenting it. Deploy the pristine core/home/config tree to
   ~/.local/share/nomarchy/config via xdg.dataFile and read from there, so it
   works without a source checkout; its live caller nomarchy-refresh-fastfetch
   now succeeds. Fix two stale SKILL.md examples (waybar/, hypr/) that pointed
   at non-existent stock paths.

2. nomarchy-docs-scripts shipped a stale divergent copy in
   features/scripts/utils/ (in the user nomarchy-system-scripts package)
   beside the canonical bin/utils dev tool — it errored outside the repo.
   Grounding it surfaced the identical bug in nomarchy-docs-keybindings.
   Delete both duplicates, add them to the generator's self-reference
   denylist so they don't show as false `missing`, regenerate docs/SCRIPTS.md.

3. Home ~/.config/nomarchy/state.json was never seeded on non-installer
   systems, so nomarchy-installed-summary rendered "—" for theme/font/panel.
   Add an idempotent home-manager activation seed in core/home/state.nix that
   backfills the resolved values (defaults * existing — user choices and
   runtime-only keys like welcome_done always win).

Verified: flake check + full eval matrix clean; refresh-config happy/error
paths and the seed deep-merge proven by hand.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

core/home/configs.nix

@@ -95,4 +95,12 @@ in
   home.file.".XCompose" = lib.mkDefault {
     source = ./config/nomarchy/default/xcompose;
   };
+
+  # Pristine copy of the stock configs, kept out of ~/.config so a user edit
+  # never touches it. `nomarchy-refresh-config` restores a file in ~/.config
+  # from here, and SKILL.md points users at it to diff against defaults.
+  xdg.dataFile."nomarchy/config".source = builtins.path {
+    name = "nomarchy-config";
+    path = ./config;
+  };
 }