This patch fixes the "Message ID alias capacity exceeded" crash (closes #549) by reordering the createChatMessageTransformHandler pipeline.

Root Cause

In lib/hooks.ts, assignMessageRefs ran before prune. Every message in the conversation received an mXXXX alias via assignMessageRefs, but then prune (via filterCompressedRanges) removed some messages from the array — those now-orm messages never got their aliases cleaned up from state.messageIds. Over a long session, these orphan aliases accumulated until the 9999-ref limit was hit, crashing the session.

Fix

lib/hooks.ts: Moved assignMessageRefs(state, output.messages) from before prune() to after it. Now only survivors of the prune pass get aliases. No alias leak, no capacity exhaustion.

- assignMessageRefs(state, output.messages)
  syncCompressionBlocks(state, logger, output.messages)
  syncToolCache(state, config, logger, output.messages)
  buildToolIdList(state, output.messages)
  prune(state, logger, config, output.messages)
+ assignMessageRefs(state, output.messages)

Verification

• tests/message-ids.test.ts: Added a RED→GREEN integration test that goes through createChatMessageTransformHandler with real prune state. On the old pipeline order the test FAILs (proving the leak); on the new order it PASSes.
• npm test: 87/87 pass
• npm run typecheck: clean