fix(deps): strip Gitea registry refs and bump to crates.io versions (mirror terraphim-kg-agents#654e707)

[AlexMikhalev]

Summary

Fixes the unbuildable state of terraphim-agents from a crates.io-only checkout. The workspace was pinned to old versions that only existed in the terraphim Gitea registry, plus had , registry = "terraphim" references in 12 dep declarations and a [registries.terraphim] block in .cargo/config.toml. Combined, this produced a "resolved to more than one candidate" error on cargo check (and a downstream E0308 expected &Thesaurus, found Thesaurus error in crates/terraphim_agent/src/service.rs).

What this PR does

Mirrors the fix that was already applied to terraphim-kg-agents in commit 654e707 ("chore: strip Gitea registry refs for crates.io pub"):

1. .cargo/config.toml — drop the [registries.terraphim] block
2. Workspace + per-crate Cargo.toml — drop , registry = "terraphim" from 12 + 16 = 28 dep declarations
3. Workspace + per-crate Cargo.toml — bump terraphim_* versions to the latest on crates.io:
   • terraphim_types 1.20.2 → 1.20.4
   • terraphim_settings 1.0.0 → 1.20.4
   • terraphim_persistence 1.20.2 → 1.20.4
   • terraphim_config 1.20.2 → 1.20.4
   • terraphim_automata 1.20.2 → 1.20.4
   • terraphim_middleware 1.0.0 → 1.20.3
   • terraphim_rolegraph 1.20.2 → 1.20.4
   • terraphim_update 1.20.2 → 1.20.4
   • terraphim_hooks 1.20.2 → 1.20.4
   • terraphim_test_utils 1.20.2 → 1.20.3
   • terraphim_sessions 1.20.4 → 1.21.1
4. Drop the terraphim_mcp_search = "0.1.2" dep + its pub use re-export from crates/terraphim_agent. The 0.1.2 version was Gitea-registry-only; the 0.2.0 on crates.io has a different API. The re-export was not referenced anywhere in the workspace.
5. Drop the terraphim_* entries from the [patch.crates-io] block in workspace Cargo.toml.

Verification

$ cargo check --message-format=short
... (compiles)
Finished `dev` profile [unoptimized + debuginfo] target(s) in 4.31s

cargo check passes (was previously failing with 3× E0308 type errors downstream of the dual-version conflict).

References

• Companion fix in terraphim-kg-agents at commit 654e707
• Same pattern likely affects terraphim-service, terraphim-core, terraphim-config-persistence, terraphim-ai — sweep in progress