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fix(state.db): recover from malformed sqlite_master so hidden sessions reappear (#43149) 
* fix(state.db): recover from malformed sqlite_master so hidden sessions reappear

The corruption class behind "Desktop/Dashboard show no sessions while
hundreds of session files sit on disk" is a malformed sqlite_master — most
often a duplicate object row, e.g. two CREATE VIRTUAL TABLE messages_fts
entries — surfacing as:

    sqlite3.DatabaseError: malformed database schema (messages_fts) -
    table messages_fts already exists

SQLite parses the whole schema while preparing the FIRST statement on a
connection, so on this class every statement fails before it runs: PRAGMA
journal_mode (which is where SessionDB.__init__ actually trips, in
apply_wal_with_fallback, BEFORE _init_schema), PRAGMA integrity_check, and
even DROP TABLE. The only operations that still work are
PRAGMA writable_schema=ON plus direct sqlite_master surgery. A plain
FTS-index rebuild at the _init_schema layer therefore cannot reach or fix
this; the canonical sessions/messages rows are intact — only the derived
schema is broken.

Add a dedicated recovery that operates where the failure actually happens:

- hermes_state.repair_state_db_schema(): backs up the raw file first, then a
  least-destructive ladder — (1) de-duplicate sqlite_master keeping the
  lowest rowid per object (preserves the existing FTS index), escalating to
  (2) drop every messages_fts* schema object + VACUUM and let the next open
  rebuild the FTS index from messages. sessions/messages are never modified.
  Plus is_malformed_db_error() to discriminate this class.
- SessionDB.__init__ auto-heals: on a malformed-schema open error it repairs
  once (process-guarded against loops / concurrent web_server opens) and
  reopens, so Desktop/Dashboard recover on their own instead of silently
  showing "no sessions".
- hermes doctor --fix detects the malformed class and repairs it (reporting
  the recovered session count + backup name).
- hermes sessions repair [--check-only] [--no-backup] runs on the raw file
  path, since SessionDB() itself cannot open a malformed DB.

Supersedes #32589 and #33869: both targeted FTS corruption but gated their
repair behind statements (integrity_check / SELECT / DROP TABLE) that
themselves fail on this class, and neither addressed the apply_wal_with_fallback
open-time failure. Credit preserved via Co-authored-by.

Closes #33865.

Co-authored-by: João Vitor Cunha <145560011+plcunha@users.noreply.github.com>
Co-authored-by: Tuna Dev <273476039+tuancookiez-hub@users.noreply.github.com>

* test(state.db): cover strat-B escalation + unrepairable safe-fail paths

---------

Co-authored-by: João Vitor Cunha <145560011+plcunha@users.noreply.github.com>
Co-authored-by: Tuna Dev <273476039+tuancookiez-hub@users.noreply.github.com>
2026-06-09 18:49:08 -05:00
..
acp feat(acp): emit session provenance metadata for compression rotation (#41724) 2026-06-07 22:22:21 -07:00
acp_adapter feat(azure-foundry): add Microsoft Entra ID auth 2026-05-18 10:14:38 -07:00
agent fix(anthropic): default new Claude models to the modern thinking contract (#42991) 2026-06-09 23:37:23 +05:30
cli test(cli): exercise real _prompt_text_input for native-Windows confirm deadlock 2026-06-08 15:53:28 -07:00
cron feat(cron): title cron sessions from the job, not the [IMPORTANT] hint 2026-06-06 12:51:12 -05:00
docker feat(dashboard): always enable embedded chat; remove dashboard --tui flag 2026-06-04 03:03:35 -07:00
e2e chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
fakes fix: streaming tool call parsing, error handling, and fake HA state mutation 2026-03-14 14:27:20 +03:00
fixtures/plugins/example-dashboard/dashboard feat(dashboard): nous-blue theme, bulk sessions, schedule picker (#37383) 2026-06-02 12:37:40 -04:00
gateway fix(gateway): cap terminal code-block preview in non-verbose mode (#42729) 2026-06-09 02:28:47 -07:00
hermes_cli fix(models): keep curated Anthropic aliases in /model picker (#43103) 2026-06-09 14:45:19 -07:00
hermes_state feat(session_search): single-shape tool with discovery, scroll, browse — no LLM (#27590) 2026-05-17 23:28:45 -07:00
honcho_plugin fix(plugins): thread-safe lazy-singleton helpers; fix honcho TOCTOU (#24759) (#42150) 2026-06-08 09:35:22 -07:00
integration refactor(gateway): migrate Home Assistant adapter to bundled plugin 2026-06-06 11:46:24 -07:00
openviking_plugin fix(openviking): add missing /agent/{agent}/ segment to memory URI — fixes #36969 2026-06-04 17:40:33 -07:00
plugins fix(photon): production hardening for the gRPC-native iMessage channel (#42732) 2026-06-09 11:12:58 -04:00
providers fix(openrouter): never send reasoning field for adaptive Anthropic models (#43012) 2026-06-10 00:18:23 +05:30
run_agent fix(codex): record app-server token usage in session accounting 2026-06-09 02:46:04 -07:00
scripts fix(skills-hub): stop shipping a degenerate index when GitHub taps collapse (#42347) 2026-06-08 15:21:28 -07:00
skills fix(google-workspace): fall back to uv when venv has no pip (#39516) 2026-06-05 13:30:02 +10:00
stress chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
tools fix(terminal): complete sane PATH entries on POSIX (salvage of #35614) (#42653) 2026-06-09 02:21:12 -07:00
tui_gateway fix(desktop): rebind sessions after websocket reconnect (salvage of #41740) (#43004) 2026-06-09 19:01:00 +00:00
website feat(skills): fix browse cap, add source links + copy buttons + category cleanup (#37143) 2026-06-01 19:52:28 -07:00
__init__.py A bit of restructuring for simplicity and organization 2025-10-01 23:29:25 +00:00
conftest.py fix: batch of small robustness/correctness fixes from @kyssta-exe 2026-06-01 19:51:03 -07:00
run_interrupt_test.py fix: thread safety for concurrent subagent delegation (#1672) 2026-03-17 02:53:33 -07:00
test_account_usage.py feat(account-usage): add per-provider account limits module 2026-04-21 01:56:35 -07:00
test_atomic_replace_symlinks.py refactor: consolidate symlink-safe atomic replace into shared helper 2026-04-28 04:58:22 -07:00
test_base_url_hostname.py security(runtime_provider): close OLLAMA_API_KEY substring-leak sweep miss (#13522) 2026-04-21 06:06:16 -07:00
test_batch_runner_checkpoint.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_bitwarden_secrets.py fix(bitwarden): prevent zip-slip path traversal when extracting bws binary (#40569) 2026-06-06 18:33:44 -07:00
test_cli_file_drop.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_cli_manual_compress.py fix(tests): catch up six stale tests after compression/aux/kanban changes (#28465) 2026-05-18 21:43:59 -07:00
test_cli_skin_integration.py fix(ci): stabilize main test suite regressions (#17660) 2026-04-29 23:18:55 -07:00
test_ctx_halving_fix.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_dashboard_sidecar_close_on_disconnect.py fix(tui-gateway): reap leaked slash_worker sessions on disconnect + active_list liveness (re-scoped onto current main) 2026-06-08 10:02:05 -07:00
test_desktop_mac_entitlements.py test(desktop): assert macOS device entitlements are inherited 2026-06-03 07:32:00 +07:00
test_docker_home_override_scripts.py feat(dashboard): always enable embedded chat; remove dashboard --tui flag 2026-06-04 03:03:35 -07:00
test_docker_stage2_browser_discovery.py fix(docker): discover Playwright headless_shell browser (#35717) 2026-06-01 16:06:44 +10:00
test_dockerfile_tini_compat_shim.py fix(docker): add /usr/bin/tini compatibility shim for legacy wrappers (#34192) (#34382) 2026-06-01 13:32:55 +10:00
test_empty_model_fallback.py test(models): guard Nous silent default against expensive-flagship escalation 2026-06-05 02:54:34 -07:00
test_env_loader_secret_sources.py fix(secrets): only apply external secrets once per HERMES_HOME per process (#32271) 2026-05-25 15:18:55 -07:00
test_evidence_store.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_gateway_streaming_nested_config.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_get_tool_definitions_cache_isolation.py fix(gateway): close residual memory-leak sites under heavy scheduled workload 2026-06-08 06:32:42 -07:00
test_hermes_bootstrap.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_hermes_constants.py fix(constants): use windows native default hermes home 2026-06-03 19:37:29 -07:00
test_hermes_home_profile_warning.py fix(constants): warn once when get_hermes_home() falls back under an active profile (#18746) 2026-05-02 01:49:55 -07:00
test_hermes_logging.py fix(gateway): tolerate Unicode in stderr log handlers on Windows 2026-06-06 19:57:44 -07:00
test_hermes_state.py fix(cron): bound the desktop run-history query to one job (#41088) 2026-06-07 02:41:01 -07:00
test_hermes_state_compression_locks.py fix(compression): prevent session-id fork from concurrent compressions (#34351) 2026-05-28 21:40:39 -07:00
test_hermes_state_wal_fallback.py fix(kanban): skip redundant WAL pragma on already-WAL connections 2026-05-27 14:31:55 -07:00
test_honcho_client_concurrency.py fix(plugins): thread-safe lazy-singleton helpers; fix honcho TOCTOU (#24759) (#42150) 2026-06-08 09:35:22 -07:00
test_honcho_client_config.py fix(honcho): harden self-hosted setup paths 2026-05-29 22:29:48 -07:00
test_honcho_session_context.py fix(honcho): align user context peer perspective 2026-05-27 10:49:33 -07:00
test_honcho_startup_fail_open.py fix: make Honcho startup fail open 2026-06-01 20:13:42 -07:00
test_install_no_initial_commit.py fix(install): move broken checkout aside instead of deleting it 2026-06-08 02:18:21 -07:00
test_install_sh_browser_install.py fix(install): support non-sudo service-user installs on apt distros (#25814) 2026-05-14 09:05:31 -07:00
test_install_sh_pythonpath_sanitization.py fix: harden install.sh against inherited Python env leakage 2026-05-06 04:02:02 -07:00
test_install_sh_root_fhs_uv_python_path.py test(install): harden uv-python-path regression test against future drift 2026-05-27 13:55:51 -07:00
test_install_sh_setup_wizard_tty_probe.py fix(install): widen /dev/tty open-probe to sibling gates (#16746) 2026-04-28 06:45:55 -07:00
test_install_sh_symlink_stomp.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_install_sh_termux_network_prereqs.py fix: strengthen termux install network prerequisites 2026-05-07 13:04:08 -07:00
test_ipv4_preference.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_lazy_session_regressions.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_lint_config.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_live_system_guard_self_test.py chore: ruff auto-fix PLR6201 resweep — tuple → set in membership tests (#27355) 2026-05-17 02:29:41 -07:00
test_mcp_serve.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_mini_swe_runner.py fix(kimi): omit temperature entirely for Kimi/Moonshot models (#13157) 2026-04-20 12:23:05 -07:00
test_minimax_model_validation.py fix(models): validate MiniMax models against static catalog (#12611, #12460, #12399, #12547) 2026-04-19 22:44:47 -07:00
test_minimax_oauth.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_minisweagent_path.py chore: remove all remaining mini-swe-agent references 2026-03-24 08:19:23 -07:00
test_model_picker_scroll.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_model_tools.py feat(middleware): add adaptive execution intercepts 2026-06-03 11:22:06 -07:00
test_model_tools_async_bridge.py fix(web): run URL SSRF checks off the event loop in async paths 2026-06-04 18:04:47 -07:00
test_ollama_num_ctx.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_output_cap_parsing.py test(agent): cover char-based output-cap overflow parsing (#42741) 2026-06-09 03:17:12 -07:00
test_package_json_lazy_deps.py fix(update): make Camofox lazy-installed instead of eager (#27055) 2026-05-16 12:15:45 -07:00
test_packaging_metadata.py fix(packaging): ship optional-mcps catalog in wheel and sdist (#39859) 2026-06-09 14:03:20 -04:00
test_plugin_skills.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_plugin_utils.py fix(plugins): thread-safe lazy-singleton helpers; fix honcho TOCTOU (#24759) (#42150) 2026-06-08 09:35:22 -07:00
test_process_loop_event_loop_warning.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_project_metadata.py fix(deps): align anthropic extra pin with lazy pin + guard whole pin surface (#42335) 2026-06-08 12:11:54 -07:00
test_retry_utils.py feat(agent): add jittered retry backoff 2026-04-08 00:41:36 -07:00
test_run_tests_parallel.py test: use subprocesses for each test file (#29016) 2026-05-21 16:40:04 +05:30
test_sanitize_tool_error.py security: sanitize tool error strings before injecting into model context (#26823) 2026-05-16 00:57:39 -07:00
test_slash_worker_watchdog.py feat(slash-worker): self-terminate on parent death via create_time watchdog 2026-06-08 07:03:12 -07:00
test_sql_injection.py fix(security): eliminate SQL string formatting in execute() calls 2026-03-19 15:16:35 +01:00
test_state_db_malformed_repair.py fix(state.db): recover from malformed sqlite_master so hidden sessions reappear (#43149) 2026-06-09 18:49:08 -05:00
test_subprocess_home_isolation.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_termux_all_extra_compat.py fix: add termux-all install profile and safe fallbacks 2026-05-07 13:04:08 -07:00
test_timezone.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_toolset_distributions.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_toolsets.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_trajectory_compressor.py fix(research): keep tool_call/tool_response pairs intact when compressing trajectories 2026-06-07 05:01:27 -07:00
test_trajectory_compressor_async.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_transform_llm_output_hook.py test+docs: cover transform_llm_output hook + release author map 2026-05-07 05:46:05 -07:00
test_transform_tool_result_hook.py test: stub has_hook in transform_tool_result hook tests 2026-06-03 06:36:46 -07:00
test_tui_gateway_server.py feat(desktop+gateway): remote-gateway file attachments via file.attach 2026-06-09 00:03:49 -07:00
test_tui_gateway_ws.py fix: resolve rebase conflict in _teardown_session worker cleanup 2026-06-08 10:02:05 -07:00
test_utils_truthy_values.py Gate tool-gateway behind an env var, so it's not in users' faces until we're ready. Even if users enable it, it'll be blocked server-side for now, until we unlock for non-admin users on tool-gateway. 2026-03-30 13:28:10 +09:00
test_web_server.py fix(tui-gateway): reap leaked slash_worker sessions on disconnect + active_list liveness (re-scoped onto current main) 2026-06-08 10:02:05 -07:00
test_wheel_locales_e2e.py fix(packaging): ship locales/ i18n catalogs in wheel, sdist, and Nix (#38383) 2026-06-03 12:00:27 -07:00
test_yuanbao_integration.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_yuanbao_markdown.py yuanbao platform (#16298) 2026-04-26 18:50:49 -07:00
test_yuanbao_pipeline.py test(yuanbao): add missing patch import to pipeline tests 2026-06-09 03:17:00 -07:00
test_yuanbao_proto.py chore: prune unused imports and duplicate import redefinitions 2026-05-28 22:26:25 -07:00
test_yuanbao_shutdown.py fix(yuanbao): bound ws.close() so an idle server can't stall shutdown ~5s (#40607) 2026-06-07 17:49:38 -07:00