fix(fsx): replace bare os.WriteFile with atomic staged replacement

[pablontiv]

Summary

• add a shared sibling-temp-file atomic write and copy utility
• convert init, migrate, scaffold, rename, and template writes to atomic replacement
• preserve existing destination permissions and document the per-file atomicity boundary

Changes

File	Change
internal/fsx/atomic.go	Adds atomic write/copy helpers with flush, mode preservation, rename, and cleanup
cmd/rootline/init.go, cmd/rootline/migrate.go	Uses atomic replacement for generated .stem files
internal/migrate/, internal/templates/	Uses the shared helper for generated documents and template copies
docs/, .claude/skills/rootline/	Documents per-file atomicity and its non-transactional boundary

Test Plan

• just test
• just check
• just coverage-check (TOTAL: 89.5%; internal/fsx: 85.4%)
• Deterministic partial-write test proves the original destination remains intact

Contributor Checklist

• Linked an approved issue
• Added exactly one type:* label
• No shell scripts changed
• Rootline skill synchronized
• Docs updated for changed behavior
• Conventional commit format
• No Co-Authored-By trailers

Fixes #106