fix: clear tool output and attachments during compaction prune

[guazi04]

Problem

When compaction prunes old tool outputs, only the time.compacted timestamp was being set — the actual output string and attachments array remained in storage indefinitely. This caused unbounded storage growth.

Evidence:

• Database size: 774 MB after 3 weeks of usage
• Storage breakdown: 81% part data (unpruned outputs), 0.07% summaries
• Duplicate tool invocations accumulating due to incomplete pruning

Solution

This PR clears the actual data when marking parts as compacted:

1. compaction.ts (2 lines):

   • Clear output and attachments array in prune() when setting time.compacted

2. prompt.ts (2 calls):

   • Add prune() calls before both compaction triggers to reduce context before LLM summarization
   • Reduces token count and storage footprint simultaneously

3. Tests (new coverage):

   • Verify prune clears output/attachments when compaction.enabled=true
   • Verify prune respects compaction.enabled=false (skips clearing)
   • Test integration with both compaction trigger points

Testing

• Unit tests: prune() behavior with/without config
• Test fixtures cover clearing behavior verification
• No breaking changes to existing API

Fixes part of #16101

[github-actions]

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[github-actions]

The following comment was made by an LLM, it may be inaccurate:

Based on my search, I found related PRs that address similar issues:

Potentially Related PRs:

1. PR fix: resolve memory leak issues across multiple subsystems #14650 - "fix: resolve memory leak issues across multiple subsystems"

   • fix: resolve memory leak issues across multiple subsystems #14650
   • Addresses memory leaks which could relate to unbounded storage growth

2. PR fix: clear tool output and attachments when pruning to prevent memory leak #7049 - "fix: clear tool output and attachments when pruning to prevent memory leak"

   • fix: clear tool output and attachments when pruning to prevent memory leak #7049
   • Very similar title addressing the exact same issue (clearing tool output and attachments)

3. PR feat(opencode): prune old tool outputs before compaction #14827 - "feat(opencode): prune old tool outputs before compaction"

   • feat(opencode): prune old tool outputs before compaction #14827
   • Related to pruning tool outputs before compaction

Note: PR #7049 appears to be addressing the same core problem (clearing tool output and attachments to prevent memory/storage leaks). You should verify if this is a duplicate or if PR #16162 is an update/fix to the previous approach.

[guazi04]

Superseded by #16175 which includes this fix plus the full MVP (CLI commands, VACUUM support, cross-project cascade fix).