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/config/nomarchy-skill/SKILL.md

@@ -57,7 +57,7 @@ This directory contains Nomarchy's source files managed by git. Any changes will
 
 **Reading `~/.local/share/nomarchy/` is SAFE and useful** - do it freely to:
 - Understand how nomarchy commands work: `cat $(which nomarchy-theme-set)`
-- See default configs before customizing: `cat ~/.local/share/nomarchy/config/waybar/config.jsonc`
+- See default configs before customizing: `cat ~/.local/share/nomarchy/config/fastfetch/config.jsonc`
 - Check stock theme files to copy for customization
 - Reference default hyprland settings: `cat ~/.config/nomarchy/default/hypr/*`
 
@@ -370,8 +370,9 @@ nomarchy-upload-log
 nomarchy-refresh-<app>
 
 # Refresh specific config file
-# config-file path is relative to ~/.config/
-# eg. nomarchy-refresh-config hypr/hyprlock.conf will refresh ~/.config/hypr/hyprlock.conf
+# config-file path is relative to ~/.config/; the stock copy must exist under
+# ~/.local/share/nomarchy/config/ (i.e. a core/home/config item).
+# eg. nomarchy-refresh-config fastfetch/config.jsonc refreshes ~/.config/fastfetch/config.jsonc
 nomarchy-refresh-config <config-file>
 
 # Full reinstall of configs (nuclear option)