fix: exclude non-wiped dirs from custom-file scan; warn on non-Claude model profiles (#2511)

* fix(detect-custom-files): exclude skills and command dirs not wiped by installer (closes #2505)

GSD_MANAGED_DIRS included 'skills' and 'command' directories, but the
installer never wipes those paths. Users with third-party skills installed
(40+ files, none in GSD's manifest) had every skill flagged as a "custom
file" requiring backup, producing noisy false-positive reports on every
/gsd-update run.

Removes 'skills' and 'command' from both gsd-tools.cjs and the SDK's
detect-custom-files.ts. Adds two regression tests confirming neither
directory is scanned.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(settings): warn that model profiles are no-ops on non-Claude runtimes (closes #2506)

settings.md presented Quality/Balanced/Budget model profiles without any
indication that these tiers map to Claude models (Opus/Sonnet/Haiku) and
have no effect on non-Claude runtimes (Codex, Gemini CLI, OpenRouter).
Users on Codex saw the profile chooser as if it would meaningfully select
models, but all agents silently used the runtime default regardless.

Adds a non-Claude runtime note before the profile question (shown in
TEXT_MODE, the path all non-Claude runtimes take) explaining the profiles
are no-ops and directing users to either choose Inherit or configure
model_overrides manually. Also updates the Inherit option description to
explicitly name the runtimes where it is the correct choice.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

get-shit-done/bin/gsd-tools.cjs

@@ -1204,10 +1204,6 @@ async function runCommand(command, args, cwd, raw, defaultValue) {
         'agents',
         path.join('commands', 'gsd'),
         'hooks',
-        // OpenCode/Kilo flat command dir
-        'command',
-        // Codex/Copilot skills dir
-        'skills',
       ];
 
       function walkDir(dir, baseDir) {