fix(context-budget): stop double-counting home skills and CLAUDE.md

[ozymandiashh]

Context-budget accuracy fix from the systematic audit (find -> verify -> adversarial -> manual confirmation + mutation check).

When the project directory IS the home directory, countSkills built [~/.claude/skills, <project>/.claude/skills] - the same path twice - and counted every skill twice; scanMemoryFiles likewise read ~/.claude/CLAUDE.md twice. The context-budget token estimate (skills + memory) was inflated for anyone running from their home dir. Both are now deduped by resolved path.

Mutation-checked: a single home skill counts 2 before the fix and 1 after; the second test confirms a genuinely distinct project skill still counts separately. tsc --noEmit clean.

[iamtoruk]

Reviewed on the merged tree. Correct accuracy fix: when the project dir is the home dir, countSkills built the same skills path twice and scanMemoryFiles read ~/.claude/CLAUDE.md twice, inflating the context-budget token estimate. Both now dedupe by path (path.join already normalizes trailing slashes and .. segments, so the identical strings collapse). Dedup fires only on identical paths, so it can only remove a double-count, never under-count a genuinely distinct project skill. Mutation-checked: reverting the skills dedup makes the one-home-skill case count 2 instead of 1; the sibling test confirms a distinct project skill still counts separately. tsc clean. Good to merge.