fix(cli): wrap a commented config, and rewrite only the entries wrapped

[Cedric921]

Closes #84.

What this changes

server-configs.ts read with JSON.parse and wrote with JSON.stringify(next, null, 2). Two consequences:

• A config with one comment was never governed. VS Code and Cline write JSONC. JSON.parse threw on the first //, the file was skipped, and its servers stayed off the proxy — no message beyond them not appearing in the list. That is the worse half: it is a reach mcp wrap claims to cover and silently does not.
• Every line changed. A four-space file came back at two spaces, so the diff a person reviews after mcp wrap touched the whole file.

Configs are now read with jsonc-parser (comments and trailing commas allowed; a file that still will not parse is left exactly alone), and written by span through a new mcp/json-span.ts, using the indentation helper agents/managed-json.ts already has. Only the wrapped entries' text changes.

The part span editing alone does not get right

I measured before writing this. jsonc-parser keeps comments and indentation, but an args array written inline — "args": ["-y", "gh-mcp"] — comes back on five lines after a wrap and an unwrap. So span edits by themselves do not meet "unwrap stays byte-identical".

unwrap deliberately rebuilds each entry from the wrapped one, not from the backup, so it survives --purge. That stays. On top of it: before writeRelaunches replaces the backup, it reads it, and where the backup still holds an entry whose value equals the one being restored — compared with canonicalJson, since key order is not part of the value — that entry's original text is spliced back in. Otherwise (after a purge, or if the entry changed) it falls back to the span edit, which is still correct and still touches only that entry's lines.

How it was verified

In mcp-command.test.ts, against two hand-written fixtures — one with comments, a trailing comma and an inline array, one in plain four-space JSON:

• the commented file is wrapped and both comments survive
• for each fixture, every line before the wrapped entry and every line after it is unchanged, and no line is indented at two spaces
• for each fixture, wrap then unwrap returns the exact original bytes
• a file that will not parse even as JSONC is left untouched

Four fail on main — including the plain-JSON reformatting and round trip, which main does parse and then rewrites. The existing round-trip test for a two-space file still passes.

prettier, tsc and knip clean. Full suite on Node 24: every failing file also fails on main here (the Noise pairing tests, which need the native addon; no Rust on this machine).

Checklist

• pnpm format && pnpm typecheck && pnpm test && pnpm deadcode all pass (Noise tests aside)
• Behaviour change ships with a test
• No any, no magic values, no console.* outside cli-output.ts
• If this touches the decision path: n/a — though more servers now reach the proxy that rules on them
• If this changes a verb table: n/a
• If this changes a command, flag or file it writes: mcp wrap now writes JSONC files it used to skip, and writes less of each file; the changeset names both