fix: dedupe files_touched at the checkpoint write boundary

[MuskanPaliwal]

this is the dedupe half of #1937, split into its own pr after @Soph asked to keep the gitrepo fix separate (comment). the underlying report is #1927: a single checkpoint metadata.json grew to 111.79 MB, 94% of it files_touched, holding 1,292,257 entries of which only 67,340 were unique — a 19x duplication factor. once that blob crossed github's 100 MB limit, entire/checkpoints/v1 became permanently unpushable, and the failure only surfaced as a warning tacked onto unrelated pushes.

what this does

writeSessionToSubdirectory used to write opts.FilesTouched into the session metadata exactly as handed to it. it now runs the list through NormalizeFilesTouched first: dedupe, sort, normalize to forward slashes. on the issue's measured numbers that alone takes the blob from 111.79 MB to about 5.5 MB and back under the limit.

a few details that came out of review on #1937 (thanks @ecgang):

• the helper preserves nil-versus-empty. files_touched is marshaled without omitempty, so nil stays JSON null and a non-nil empty list stays [] — the wire format is unchanged for empty inputs.
• both live backends inherit the fix through the shared treeWriter (gitRefsStore embeds it), and the test now runs against both the git-branch and git-refs stores instead of leaning on the embedding argument.
• the fsstore reference backend applies the same normalization, since it's the worked example the next real backend would copy.

why it warns instead of deduping silently

soph's worry on #1937 was that a silent dedupe hides the actual bug, and it's a fair worry: every merge path in the current code already dedupes — i audited them, and @ecgang audited them independently and came up equally empty (their comment on #1927 lists the paths) — so whatever produced the 19x duplication is either a version older than 0.8.42 or a path nobody has found yet. so when the boundary strips duplicates, it now logs a warning with the session id and the reported-versus-unique counts. if a live producer exists, it shows up in .entire/logs instead of disappearing into the dedupe.

tests

• TestWriteCommitted_DeduplicatesFilesTouched: duplicated input written, permanent record read back deduplicated and sorted, against both git backends. fails without the boundary dedupe.
• empty-input cases pin the nil-versus-[] behavior.
• mise run check green: fmt, lint, unit, integration, and the e2e canary.

what this does not do

it can't repair a branch that already carries an oversized blob — git history is immutable, so an affected entire/checkpoints/v1 needs a one-time rewrite, as discussed on the issue. and it deliberately doesn't touch the nested-checkout walking, which is the other (unbounded) half of the issue and lives in #1937.

🤖 Generated with Claude Code

[Soph]

Thanks!