cli: programmatic ergonomics — --method initialize, --tool-args-json, --connect-timeout, env-var fixes

[cliffhall]

Summary

Programmatic-ergonomics flags and env-var fixes for the CLI:

• --method initialize — connect-only probe; prints {serverInfo, protocolVersion, capabilities, instructions}.
• --tool-args-json '{"k":"v"}' — pass tool args verbatim as JSON (no string→number coercion); mutually exclusive with --tool-arg.
• --connect-timeout <ms> — default 15000 for ad-hoc --server-url invocations, 0 (none) for catalog/config-driven runs (withConnectTimeout() helper).
• MCP_CATALOG_PATH no longer conflicts with an ad-hoc --server-url/target invocation (env catalog ignored when ad-hoc).
• MCP_STORAGE_DIR honored alongside the per-file env override.

Reference implementation (PR #1510)

Re-implement informed by these changes at 33fac3f:

• clients/cli/src/cli.ts — initialize branch in callMethod, --tool-args-json parse/merge, DEFAULT_CONNECT_TIMEOUT_MS + withConnectTimeout(), adHoc detection gating MCP_CATALOG_PATH
• clients/cli/tests/format-and-args.test.ts — initialize + tool-args-json tests

Depends on

• CLI exit-code map + error envelopes (usage errors and timeout classification build on it)

Wave 3 (CLI) lane — sequential with the other cli.ts issues; parallel to the Apps-host lane.

Notes

• Add a dedicated test for the ad-hoc vs file-based default-timeout split (the PR relies on integration coverage).
• Document new flags and env-var semantics in clients/cli/README.md (docs rule).
• Coverage gate ≥90 on all four dimensions (cli.ts is measured in-process via runCli()).

Part of the PR #1510 decomposition (see tracking issue).