fix(comm+schedule): SQL pushdown for thread, indexes, read filter (#535)

[ohdearquant]

Summary

• Thread pushdown: comm.thread now pushes $.thread_id predicate into SQL instead of scanning all messages and filtering in Rust (~30 lines of post-filter code removed)
• Dead index fix: Pack indexes changed from literal WHERE kind = 'message' to WHERE deleted_at IS NULL with kind as indexed column — SQLite can now use them with parameterized queries
• Read filter fix: New FilterOp::JsonTypeEq / JsonTypeNeMissing variants handle malformed legacy boolean values consistently via json_type() instead of extracted truthiness

Closes #535

Test plan

• 198 new integration test lines across comm and schedule packs
• Thread retrieval test verifies only thread messages returned
• Read filter handles missing, true, false, "true" (string), 1 (numeric)
• cargo test --workspace (all pass)
• cargo clippy --workspace --all-targets -- -D warnings (clean)

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