feat(clone): a sync mode, and the shared rename table birth and sync now both use

[Jammy2211]

Summary

A fresh agent chat pointed at a science project folder should work out where the
project got to, how to resume, and what its history is — by default. This is the
organ-side half of that: a sync mode on the clone conductor, so the change
lands in the sibling assistants from the reference's own diff rather than as four
hand edits.

clone sync takes the reference assistant's diff over a commit range, restricts
it to that reference's generic pattern set (reusing REFERENCE_PROFILES /
match_any — not a second list), rewrites the names for the target, and applies
it with GNU patch, reporting per file applied / created / already-applied
/ rejected (hunks #n) / absent / skipped / unsupported. Dry run by
default; --apply writes and leaves .rej files; exit 1 when anything was
rejected. "Since the sibling's last sync" is read from the sibling's own history
via a Clone-sync: <reference>@<sha> commit trailer — no state file.

The second commit closes the seam that made birth and sync disagree: birth and
sync each built their own rename list, and birth's was missing two rules.
name_substitutions() is now the one table both use, carrying the UPPERCASE
package rule birth omitted plus DOMAIN_NOUNS / DOMAIN_ALIASES (the science's
own noun, word-anchored so microlensing survives and lensing-fluent keeps its
tail). A target package absent from the table gets no domain rule and a
printed warning — a science's own noun is never guessed.

Commits on this branch:

• 55e9fd4 feat(clone): add a sync mode — replay the reference's generic diff onto the born siblings
• d2b1af9 clone sync: domain + env-var substitution rules (feat: science-project memory — a fresh chat resumes a project by default #315)

API Changes

New capability, nothing removed or renamed: bin/pyauto-brain clone sync is a
new CLI mode, and the clone conductor gains a shared name_substitutions()
rename table that both birth (apply_seed) and sync now read instead of each
building its own. Existing clone behaviour is unchanged apart from birth
picking up the two rules it was missing. See full details below.

Test Plan

• pytest tests/ -q → 634 passed (627 before this branch's second commit; tests/test_clone_sync.py 9 → 16 tests)
• Tenant firewall check OK (its allowlist entry for the new test file is already on PyAutoMind main, 2b764e48)
• Exercised end to end on live siblings: clone sync --since ee306ac --target autofit_assistant --apply reproduced its dry run exactly (1 applied · 2 created · 4 rejected)
• Dry run writes nothing; rejected hunks are reported, never auto-resolved

Full API Changes (for automation & release notes)

Added

• bin/pyauto-brain clone sync [--since <rev>] [--target <assistant>] [--apply] — replay the reference assistant's generic-file diff onto a born sibling as a reviewable three-way patch; dry run by default, exit 1 on any rejected hunk.
• agents/conductors/clone/_clone.py::name_substitutions() — the single source of the birth/sync rename table (package names incl. UPPERCASE env-var form, DOMAIN_NOUNS, DOMAIN_ALIASES).
• agents/conductors/clone/_clone.py::sync_substitutions() — sync's view of that table.
• Clone-sync: <reference>@<sha> commit trailer — how a sibling records the point it last synced from.

Changed Behaviour

• apply_seed now serialises name_substitutions() for PyAutoHands' clone_seed instead of building its own list, so a birth picks up the UPPERCASE package rule and the domain-noun rules it previously omitted.
• A target package absent from the domain table gets no domain rule plus a printed warning, rather than a guessed noun.

Migration

• None. Existing clone invocations are unaffected; sync is additive.

Closes #315.

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