Replace RuleRegistry with RuleSet and unify rule model (#102)

[matthewhorridge]

Summary

Refactor of the rule model and registry to prepare for multi-source harmonization (#90). Closes #102.

• HarmonizationRule: source: str becomes sources: List[str]. Single-source rules are the one-element case. transform() unwraps the singleton so existing primitives still receive a scalar; multi-source rules pass the full list through.
• RuleSet replaces RuleRegistry: flat list of rules keyed on target. One rule per target (warns and replaces on collision). JSON schema becomes a flat array. For migration, RuleSet.load() and HarmonizationRule.from_serialization() still accept the legacy nested {source: {target: rule}} / scalar "source": "x" formats.
• harmonize_dataset runs every rule in the RuleSet (no more harmonization_pairs). Source columns are read via df[rule.sources].apply(axis=1).
• CLI --targets becomes a load-time filter on the RuleSet. --on-missing checks every entry of rule.sources; a multi-source rule is skipped if any source is missing.
• RPC API: mode=pairs/harmonization_pairs removed (per the additional design decision in the issue thread) — the RPC always runs every rule in the rules file. To run a subset, construct a rules file containing only the desired targets. TS client types updated to match.
• utils.transformations.replay() rewritten to build a per-dataset RuleSet.
• Demo rules files migrated to the flat array schema. Rule, RuleStore, and RuleRegistry aliases removed.

Breaking changes

• JSON rule files now use a flat array (legacy nested schema still loads).
• harmonize_dataset(... harmonization_pairs=...) signature changed; harmonization_pairs is gone.
• harmonize RPC drops mode and pairs.
• Rule, RuleStore, RuleRegistry (the class) symbols are removed; import RuleSet instead.

Notes

• demo/integration.ipynb still imports an even older RuleStore/rule_store that didn't exist on main; it was already stale and is left untouched.

Test plan

• pytest — all 75 tests pass, including new coverage for legacy schema compat and multi-source transform
• demo/harmonize_example/run_example.py runs end-to-end against the migrated flat-array rules file
• Reviewer to confirm RPC breaking change is acceptable (was also discussed in the issue thread)

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