fix: make flint-setup state-based

[zeitlinger]

Summary

Make flint-setup state-based instead of version-counter-based.

flint-setup no longer persists or advances settings.setup_migration_version. Routine check mode now stays focused on current actionable setup state from mise.toml: obsolete tool-key migrations, unsupported legacy lint tools, missing node for npm: backends, and canonical [tools] ordering.

flint-setup --fix still does the heavy lifting for active setup migrations, but only when the current tool state actually activates that migration. In practice this keeps routine checks cheap and unsurprising while still letting a Flint/tool update branch apply the full migration directly.

For the markdownlint-era stack, that means fix mode removes the old tool entries and applies the repo cleanup only when those legacy tools are still present in mise.toml. Ambient stale comments in unrelated repos no longer surface as generic setup drift.

This also removes now-vestigial setup migration plumbing:

• drop settings.setup_migration_version from generated and parsed flint.toml
• remove fix-time writeback of setup migration state
• make old tool-key replacements unconditional when their legacy keys are present

Validation

• cargo test flint_setup -- --nocapture
• cargo test init::tests -- --nocapture
• cargo test registry -- --nocapture
• FLINT_CASES=general/flint-setup cargo test cases -- --nocapture
• mise run lint:fix
• mise run lint

[zeitlinger]

Superceded by #252

[zeitlinger]

Superseded by #252. The current branch and follow-up state-based flint-setup work landed there, so I’m closing this one to keep the review thread in one place.