Fix #2035: add missing doc comments to 16 crates (doc gaps 2026-06-03)

[AlexMikhalev]

Summary

Adds missing item-level `///` doc comments to eliminate all `RUSTDOCFLAGS="-W missing-docs"` warnings across all 18 crates listed in issue #2035.

Result: 0 warnings across all 18 crates

Crate	Warnings before	Warnings after
terraphim_types	1	0
haystack_jmap	1	0
haystack_core	3	0
terraphim_settings	4	0
terraphim_mcp_server	6	0
terraphim_rolegraph	11	0
terraphim_sessions	12	0
terraphim_persistence	19	0
terraphim_middleware	35	0
terraphim_config	43	0
terraphim_automata	80	0
terraphim_rlm	83	0
terraphim_grep	125	0
terraphim_service	111	0
terraphim_agent	119	0
terraphim_orchestrator	674	0
haystack_atlassian	0	0
haystack_discourse	0	0

Approach

• Enum variant docs: one sentence describing what the variant represents
• Struct field docs: one sentence describing what the field holds
• Module docs: brief description of the module's purpose
• Function/method docs: one sentence describing what the function does
• No logic or signature changes — doc comments only
• One macro-generated item in `terraphim_settings` (`twelf::config`) suppressed with `#![allow(missing_docs)]` and a comment explaining why

Verification

```bash
RUSTDOCFLAGS="-W missing-docs" cargo doc --no-deps -p 2>&1 | grep "^warning: missing"

Returns empty for all 18 crates

```

Fixes #2035 (Gitea)

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