Inline small contents in nodes (cleaned up)

[balat]

Summary

This PR continues and cleans up the inline contents feature for irmin-pack, building on:

• Inline small objects #2378 by @clecat (initial inline small objects implementation)
• Inline small contents in nodes #2390 by @cuihtlauac (inline small contents in nodes v2)

I’ve tried to tidy up the commits as much as possible, avoiding back-and-forth changes wherever possible to make them easier to review

Small content values (configurable threshold, default 48 bytes serialized) are stored directly within parent node entries rather than as separate pack file entries.

Reviewing notes

The commits have been tidied up from #2390 but one deliberate back-and-forth remains in the history:

1. The first commit (Implement inline contents) adds a contents_key list to the Node variant: `Node of node_key * contents_key list. This was part of the original design by @clecat where the inlining decision was made at tree construction time — the list was meant to track which contents had been inlined within each node, so that the GC, integrity checks, and export could handle them.

2. A later commit (Move inlining decision to export/serialization layer) changed the architecture so inlining is decided at export time instead, via should_inline_contents. This made the list redundant — it was never populated (always []) but was still threaded through the entire codebase.

3. The commit Remove unused contents_key list from Node variant removes it, simplifying 42 files and eliminating all TODO inline comments that marked the empty-list sites.

We could not squash these together without also squashing all intermediate commits (benchmarks, threshold changes, etc.), which would have made the history less readable. We chose to keep the intermediate steps visible.

Changes relative to #2390

Cleanup

• Remove -warn-error -A from root dune config
• Remove debug executable from bin/ (lavyek dependency, from another branch)
• Remove commented-out assert false debug breakpoints
• Restore Irmin_tezos.Conf in bench and tezos_explorer (PR had replaced it with local copies using wrong contents_length_header)

Bug fixes

• Restore forbid_empty_dir_persistence guard (was commented out)
• Fail explicitly on Contents_inlined in irmin-git (was silently dropping data)
• Deserialize inlined contents in libirmin contents_of_key (was returning null)

Architecture improvements

• Remove contents_key list from Node variant — see reviewing notes above
• Replace global Atomic.t with per-repo config — add Backend.Repo.inline_contents_max_bytes so each repo carries its own inlining config. This fixes the issue where opening two repos with different settings would overwrite each other's config.
• Make threshold configurable — add inline_contents_max_bytes to Irmin_pack.Conf (default 48)
• Validate configuration — reject negative inline_contents_max_bytes values

Tests

• Re-enable From_v2 upgrade test (was disabled)
• Restore original V3 test archives and hash constants (hashes are identical to pre-inlining when inlining is disabled)
• Add test for inlining with non-default metadata (exercises inlined-x-i/inlined-x-d variants)
• Add validation and edge case tests for inline_contents_max_bytes

History cleanup

• Remove thread-safety commits (belong in multicore-safety branch)
• Remove Atomic.t commit (superseded by per-repo config)
• Squash first 6 implementation commits into one (too many back-and-forth changes to review separately)
• Squash two Formatting commits into one

Test plan

• All 258 irmin-pack tests pass
• From_v2 upgrade test re-enabled and passing
• Inline contents tests (7 tests): without/with inlining, equivalence, structure, metadata, validation, edge cases
• libirmin C test for Contents_inlined (requires ctypes, not available in current env)