[codex] Fix SQLite diagnostics and query hardening

AGENT_GUIDE.md

@@ -131,7 +131,7 @@ CI watching must be bounded. Do not loop indefinitely.
 
 ## Status Contract
 
-- `status --json` and related JSON/MCP payloads currently expose the trust fields documented in `README.md` and `DEVELOPER_GUIDE.md`, including `fold_ready`, `fold_ready_reason`, `graph_table_available`, `issues_table_available`, `file_issues_data_current`, `migration_in_progress`, `sql_graph_contract_ready`, `sql_graph_contract_degraded_reason`, `hotspot_family_ready`, `hotspot_family_degraded_reason`, `language_readiness`, `csharp_symbol_name_ready`, `csharp_metadata_target_ready`, `csharp_metadata_target_degraded_reason`, `indexed_head_commit`, `worktree_head_changed`, `index_writer_version`, `index_newer_than_reader`, `index_newer_than_reader_reason`, `unknown_extension_file_count`, `unknown_extension_files`, `unknown_extension_files_truncated`, `unknown_extension_file_path_limit`, `unknown_extension_extension_counts`, `unknown_extension_category_counts`, `unknown_extension_groups`, `extractors`, `path_case_sensitive`, `data_dir`, `data_dir_source`, `data_dir_mode`, `mac_profile`, `mac_profile_diagnostics`, `db_size_bytes`, `wal_size_bytes`, `db_pragma_settings` (`journal_mode`, `synchronous`, `wal_autocheckpoint`, `page_count`, `freelist_count`, `page_size`, `auto_vacuum`), `maintenance_guidance`, `symbol_kinds`, `symbols_by_language`, status kind cap metadata (`symbol_kind_limit`, `symbol_kind_name_limit`, `symbol_kind_total_count`, `symbol_kind_omitted_count`, `symbol_kind_names_truncated`, `symbols_by_language_kind_total_counts`, `symbols_by_language_kind_omitted_counts`, `symbols_by_language_kind_names_truncated`), `process`, `last_index_run`, `last_failed_or_partial_index_run`, `last_workspace_freshened_at`, `hooks`, `hook_diagnostics`, `trust_overrides`, MCP-only `mcp_session`, and the `status --check`-only `stale_after_seconds` / `index_age_seconds` threshold audit fields and `repair_commands`.
+- `status --json` and related JSON/MCP payloads currently expose the trust fields documented in `README.md` and `DEVELOPER_GUIDE.md`, including `fold_ready`, `fold_ready_reason`, `graph_table_available`, `issues_table_available`, `file_issues_data_current`, `migration_in_progress`, `sql_graph_contract_ready`, `sql_graph_contract_degraded_reason`, `hotspot_family_ready`, `hotspot_family_degraded_reason`, `language_readiness`, `csharp_symbol_name_ready`, `csharp_metadata_target_ready`, `csharp_metadata_target_degraded_reason`, `indexed_head_commit`, `worktree_head_changed`, `index_writer_version`, `index_newer_than_reader`, `index_newer_than_reader_reason`, `unknown_extension_file_count`, `unknown_extension_files`, `unknown_extension_files_truncated`, `unknown_extension_file_path_limit`, `unknown_extension_extension_counts`, `unknown_extension_category_counts`, `unknown_extension_groups`, `extractors`, `path_case_sensitive`, `data_dir`, `data_dir_source`, `data_dir_mode`, `mac_profile`, `mac_profile_diagnostics`, `db_size_bytes`, `wal_size_bytes`, `db_pragma_settings` (`journal_mode`, `synchronous`, `wal_autocheckpoint`, `busy_timeout_ms`, `page_count`, `freelist_count`, `page_size`, `auto_vacuum`), `prepared_command_cache` (`count`, `capacity`, `hit_count`, `miss_count`, `eviction_count`), `maintenance_guidance`, `symbol_kinds`, `symbols_by_language`, status kind cap metadata (`symbol_kind_limit`, `symbol_kind_name_limit`, `symbol_kind_total_count`, `symbol_kind_omitted_count`, `symbol_kind_names_truncated`, `symbols_by_language_kind_total_counts`, `symbols_by_language_kind_omitted_counts`, `symbols_by_language_kind_names_truncated`), `process`, `last_index_run`, `last_failed_or_partial_index_run`, `last_workspace_freshened_at`, `hooks`, `hook_diagnostics`, `trust_overrides`, MCP-only `mcp_session`, and the `status --check`-only `stale_after_seconds` / `index_age_seconds` threshold audit fields and `repair_commands`.
 - When any readiness field is degraded, the CLI adds `degraded_root_cause`, `degraded_reason`, `recommended_action`, `alternative_action`, and `readiness_degradations[]`. `degraded_root_cause` is the primary stable machine code; `readiness_degradations[]` lists every degraded field with `root_cause`, human reason, and remediation strings.
 - `hotspot_family_degraded_reason` currently uses `hotspot_family_support_not_indexed`, `hotspot_family_metadata_stale`, `hotspot_family_disabled_at_index_time`, `partial_family_key_population`, and `hotspot_family_marker_fingerprint_incomplete`; the incomplete marker fingerprint code means marker traversal hit safety caps and should stay synchronized with README / developer-guide recovery notes.
 - `issues_table_available` reports physical `file_issues` table presence only. `file_issues_data_current` reports whether the table is also stamped current for the active index generation.