Runtime: bound bash logs and skip runtime mirrors

[gaofeng21cn]

Problem

Long-running bash sessions can produce oversized terminal output that bloats rendered logs and ordinary file search. Stale session reconciliation also left an empty finished_at value when the metadata key existed with null.

Solution

• Bound unterminated bash output buffers and truncate oversized single rendered terminal-log lines while keeping full content in log.jsonl.
• Compact oversized completed terminal.log files into a byte-window view, preserving the original log as a quest-local backup path and recording compaction metadata on the session.
• Fill empty finished_at during stale-session reconciliation.
• Exclude heavy runtime mirrors under .ds/bash_exec, .ds/runs, .ds/codex_history, runner homes, evidence packets, slim backups, and cold archives from default explorer search.

MDS provenance

Adapted the generic runtime-log and search-hygiene parts of MedDeepScientist commits 60b8f07, 530ebb7, and b868449. MedDeepScientist, MAS, medical-fork, manuscript-readiness, and publication-authority semantics were intentionally excluded.

Tests

• python -m py_compile src/deepscientist/bash_exec/monitor.py src/deepscientist/bash_exec/service.py src/deepscientist/quest/service.py
• git diff --check
• uv run --with pytest pytest -q tests/test_bash_exec_monitor.py tests/test_memory_and_artifact.py::test_explorer_search_skips_heavy_runtime_mirrors_by_default tests/test_mcp_servers.py::test_bash_exec_mcp_server_default_read_truncates_long_logs_with_hint tests/test_mcp_servers.py::test_bash_exec_mcp_server_read_supports_start_and_tail_windows tests/test_mcp_servers.py::test_bash_exec_mcp_server_seq_tail_reports_remaining_seq_ranges tests/test_daemon_api.py::test_bash_exec_handlers_expose_sessions_logs_and_stop