Fix MCP initialize and logging gaps

AGENT_GUIDE.md

@@ -123,14 +123,15 @@ 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`, `sql_graph_contract_ready`, `sql_graph_contract_degraded_reason`, `hotspot_family_ready`, `hotspot_family_degraded_reason`, `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`, `path_case_sensitive`, `data_dir`, `data_dir_source`, `data_dir_mode`, `mac_profile`, `db_pragma_settings` (`journal_mode`, `synchronous`, `wal_autocheckpoint`, `page_count`, `freelist_count`, `page_size`), `hooks`, and the `status --check`-only `stale_after_seconds` / `index_age_seconds` threshold audit fields.
+- `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`, `sql_graph_contract_ready`, `sql_graph_contract_degraded_reason`, `hotspot_family_ready`, `hotspot_family_degraded_reason`, `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`, `path_case_sensitive`, `data_dir`, `data_dir_source`, `data_dir_mode`, `mac_profile`, `db_pragma_settings` (`journal_mode`, `synchronous`, `wal_autocheckpoint`, `page_count`, `freelist_count`, `page_size`), `hooks`, MCP-only `mcp_session`, and the `status --check`-only `stale_after_seconds` / `index_age_seconds` threshold audit fields.
 - When `fold_ready` or `csharp_metadata_target_ready` is the only degraded readiness bit, the CLI also adds `degraded_reason`, `recommended_action`, and `alternative_action`.
 - `index_writer_version` records the `cdidx` version that last wrote to the DB (stamped into `codeindex_meta` as `cdidx_writer_version` on every full scan, update, and MCP index). `index_newer_than_reader` flips to `true` whenever any persisted numeric contract stamp in `codeindex_meta` (or unknown `PRAGMA user_version` readiness bits) exceeds the current binary's compiled maximum, so an older CLI re-opening a DB written by a newer CLI degrades loudly with an audit trail instead of silently dropping back to text-search fallbacks. `index_newer_than_reader_reason` enumerates the specific newer-than-reader stamps.
 - `status` also surfaces indexed-HEAD freshness via `indexed_head_sha`, `indexed_head_branch`, `indexed_head_timestamp`, and `commits_ahead_of_indexed_head`. They are stamped by `cdidx index` on every successful run (full scan AND partial update, distinct from `indexed_head_commit` which is full-scan only) on a best-effort basis (never blocks an otherwise-successful index) and omitted on non-git workspaces, detached HEAD (branch only), or legacy DBs created before this contract.
 - `status` also surfaces unknown-extension scan coverage via `unknown_extension_file_count`, stamped by successful full-repository index runs (`cdidx index <projectPath>` and MCP `index_project`) as the number of non-indexed files with non-empty extensions that do not map to a known language. It is omitted on legacy DBs or before a current full scan has stamped the value.
 - `status` also surfaces `.cdidx` data-directory permissions via `data_dir_mode` on POSIX filesystems. New `.cdidx` data directories are forced to `0700`; the field is omitted on Windows, URI DBs, or when the directory mode cannot be inspected.
 - `status` also surfaces filesystem case-sensitivity via `path_case_sensitive`, stamped on every successful `cdidx index` run (full scan AND partial update, plus MCP-driven indexes) from `core.ignorecase` + a live filesystem probe. `true` means the volume is case-sensitive (`Foo.cs` and `foo.cs` are distinct); `false` means case-insensitive. Omitted on legacy DBs that predate the stamp. Use it to audit path-equality decisions on case-sensitive APFS, WSL NTFS / dev-drive, and ReFS mounts where the prior OS-keyed heuristic could mis-classify the workspace (#1546).
 - `status` also surfaces Linux mandatory-access-control context via `mac_profile` when `/proc/self/attr/current` or `/proc/self/attr/exec` indicates an AppArmor or SELinux profile. It is omitted on non-Linux hosts, unconstrained processes, or unreadable proc attributes (#1768).
+- MCP `status` also surfaces session diagnostics via `mcp_session`. It is not persisted DB state; it includes the current `log_level`, captured `roots`, and optional `client_capabilities`.
 - Keep `README.md`, `DEVELOPER_GUIDE.md`, and this file synchronized if this contract changes.
 
 ## Reference Extraction