chore: retire pramana-mcp; move to archive/ and cut from CLI + workspace

[sarath-soman]

Motivation

Follow-up to #242. With the TUI archived and a `/pramana` skill (#243) planned to wrap the primitives, the MCP layer becomes a second API shape for the same 5 operations without a load-bearing use case in this workflow:

• Three API shapes today for the same primitives: `pramana-engine` functions, CLI subcommands (`clap`), MCP tools (JSON schema). Each new primitive touches three places.
• MCP's real value is autonomous tool-use (Claude reaching for `pramana.search` mid-turn without being asked) and cross-IDE compat (Claude Desktop / Cursor / Zed). Neither is load-bearing for a Claude-Code-only workflow where interaction goes through `/pramana` skill invocations.
• Cost of carrying MCP: `pramana-mcp` crate, `rmcp` + `tokio` deps on CLI, `mcp` feature flag + its CI matrix row, e2e tests, a stdio server subprocess spawned per MCP consumer.

Lean target shape: `pramana-engine` (core) + `pramana-cli` (binary) + `/pramana` skill (human surface). Three layers, distinct jobs, no overlap.

Scope

Same pattern as #242 — move, don't delete.

Code move

• `git mv crates/pramana-mcp archive/pramana-mcp`
• Remove `"crates/pramana-mcp"` from root `Cargo.toml` `[workspace].members`
• The archive README (added in chore: retire pramana-tui; move to archive/ and cut from CLI + workspace #242) should mention this crate too

CLI excision

• `crates/pramana-cli/Cargo.toml`:
  • Drop `mcp = ["dep:pramana-mcp", "dep:tokio"]` from `[features]`
  • Drop `pramana-mcp = { path = "../pramana-mcp", optional = true }` from `[dependencies]`
  • Drop the optional `tokio` dep entirely (only used by MCP)
  • After chore: retire pramana-tui; move to archive/ and cut from CLI + workspace #242 also lands, `default = ["mcp", "tui"]` becomes `default = []`
• `crates/pramana-cli/src/main.rs`:
  • Remove the `Mcp { source }` enum variant (line ~122, behind `#[cfg(feature = "mcp")]`)
  • Remove the `Commands::Mcp { source } => cmd_mcp(source)` match arm (line ~256)
  • Remove `fn cmd_mcp(...)` (line ~282–340, includes the `rt.block_on(pramana_mcp::start_mcp_server(tm))` call)
• `crates/pramana-cli/tests/mcp_e2e.rs` — delete the file (retires with the subcommand)

CI

• `.github/workflows/ci-rust.yml`: drop the `"--no-default-features --features mcp"` row from the `features` matrix. After chore: retire pramana-tui; move to archive/ and cut from CLI + workspace #242 this shrinks the matrix to just `--no-default-features` + `--all-features` (and `--all-features` becomes equivalent to default because both `mcp` and `tui` are gone).

Docs

• `README.md`: the example MCP config block (`"args": ["mcp", "--source", "./knowledge"]`, line ~43) either (a) gets removed with a one-liner "MCP server retired; use the `/pramana` skill from Claude Code" note, or (b) stays with an explicit "archived — see `archive/pramana-mcp/` to resurrect" warning.
• `docs/rust-port.md`: remove the `mcp` row from the feature matrix (line ~46), the feature-build example (line ~56), and the `pramana-mcp/` entry in the crate-layout tree (line ~75).

Side-effects to flag

• Any existing MCP clients pointing at `pramana mcp` will break — e.g. a local `.mcp.json` entry or a Claude Desktop config. Call this out in the release notes.
• After this lands, issue feat(skill): add /pramana skill with subcommands over MCP primitives #243 needs an edit: its current spec says "MCP-first dispatch with CLI fallback only where MCP doesn't expose a surface." That becomes "Bash → CLI always; no MCP." The `/pramana` skill dispatches by shelling out for every subcommand. The subcommand table in feat(skill): add /pramana skill with subcommands over MCP primitives #243 stays as-is but the implementation path simplifies.

Non-goals

• Don't keep the archived crate buildable from `archive/` — its workspace-relative deps break on move, which is fine (same reasoning as chore: retire pramana-tui; move to archive/ and cut from CLI + workspace #242).
• Don't change the engine — the 5 primitives stay exactly as-is on `pramana-engine`. CLI wraps them; skill wraps CLI. MCP was a parallel wrapper; now it isn't.

Acceptance

• `cargo build --release -p pramana-cli` succeeds without `mcp` (or `tui`) features
• `pramana --help` no longer lists `mcp` as a subcommand
• `cargo clippy --workspace --all-targets -- -D warnings` clean
• `cargo test --workspace` passes (mcp_e2e tests disappear with the subcommand; remaining tests unaffected)
• `.github/workflows/ci-rust.yml` feature matrix passes all remaining rows
• `git log --follow archive/pramana-mcp/src/server.rs` shows full pre-archive history
• `pramana-cli` `[dependencies]` section no longer mentions `tokio` or `pramana-mcp` or `rmcp`

Ordering

Logical execution order:

1. chore: retire pramana-tui; move to archive/ and cut from CLI + workspace #242 (retire TUI)
2. This issue (retire MCP)
3. feat(skill): add /pramana skill with subcommands over MCP primitives #243 (add `/pramana` skill — revised per the "Side-effects" note above)

But nothing technically blocks picking up this issue before #242. They're independent excisions; the only shared artefact is `archive/README.md`.

Release impact

Patch bump. Release note: "MCP stdio server retired; `archive/pramana-mcp/` preserves the code. Everyday Claude usage: the `/pramana` skill wraps the CLI (see #243). Resurrect via `archive/README.md`."