cli: Wave 3 — programmatic review path (rollup of #1573–#1575) (#1655)

* feat(cli): programmatic ergonomics — initialize, tool-args-json, connect-timeout, env-var fixes

Adds the #1573 programmatic-ergonomics surface to the CLI, re-implemented
informed by PR #1510 and adapted to the v2/main OAuth-wired cli.ts:

- `--method initialize` — connect-only probe emitting
  `{serverInfo, protocolVersion, capabilities, instructions}`.
- `--tool-args-json '{"k":"v"}'` — tool args passed verbatim as JSON (no
  key=value coercion); mutually exclusive with `--tool-arg`, with clear
  errors for combined use, malformed JSON, and non-object values.
- `--connect-timeout <ms>` — default 15000 for ad-hoc `--server-url`/target
  runs, file-level timeout otherwise; `0` disables. Backed by the exported
  `withConnectTimeout()` helper.
- MCP_CATALOG_PATH is ignored when an ad-hoc target is given, so a shell that
  exports it can still run one-off ad-hoc invocations.
- MCP_STORAGE_DIR is honored by core `getStateFilePath` (`<dir>/oauth.json`),
  below the per-file MCP_INSPECTOR_OAUTH_STATE_PATH override.

Tests: new programmatic-ergonomics.test.ts (CLI, in-process runCli + direct
withConnectTimeout unit tests) and getStateFilePath resolution cases in the
web storage integration suite. Per-file coverage gate stays ≥90.
README: documents the new flags and env-var semantics.

Closes #1573

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BrihGWcrM9JGRyu41nzZYw

* feat(cli): --app-info probe + --format json envelope

Adds the #1574 app-probing and machine-readable output surface, re-implemented
informed by PR #1510 and adapted to the v2/main OAuth-wired cli.ts.

- `--method tools/call --tool-name <t> --app-info` — prints one JSON line
  describing the tool's app posture (hasApp, resourceUri, csp, permissions,
  domain, …) WITHOUT invoking the tool; exit 0 when it has an app, 2 (no_app)
  when it doesn't. A missing tool exits 5 (tool_not_found) — distinct from the
  no-app exit so a typo isn't mistaken for "no app".
- `--method tools/list --app-info` — one NDJSON line per tool over a single
  connection (`| jq -c 'select(.hasApp)'`).
- `--format json` — a single stdout envelope (`{result}` plus `{appInfo}` as a
  sibling key for App tools), no banner, so any method pipes into jq.
- A tools/call returning isError:true now exits 5 (tool_is_error) after
  printing its payload, so && chains stop on a failed call.

Implementation: `collectAppInfo()` (core `extractAppInfo` + a tolerated
resource read that reports `resourceError`), an NDJSON loop in tools/list, and
a single `emitResult()` that owns format + exit-code handling. `runMethod` now
returns a `MethodOutcome` discriminated union so the NDJSON path can signal
"already emitted".

Tests: app-info.test.ts (exit-0/2/5 + NDJSON + no-invoke), format-json.test.ts
(envelope shapes + bad --format), emit-result.test.ts (direct unit coverage of
the isError→exit-5 and resourceError branches via exported emitResult/
collectAppInfo). Updated the tools.test "nonexistent tool" case to the new
exit-5 tool_not_found contract. Per-file coverage ≥90 on all four dimensions
(cli.ts 100% stmts/funcs/lines). README documents the flags, NDJSON shape, and
exit semantics.

Closes #1574

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BrihGWcrM9JGRyu41nzZYw

* feat(cli): stored-auth suite — --use-stored-auth, --wait-for-auth, --list-stored-auth, --print-handoff

Adds the #1575 web→CLI OAuth handoff surface, re-implemented informed by PR
#1510 and adapted to v2/main.

- `--use-stored-auth` — read the shared oauth.json and inject
  `Authorization: Bearer <token>` for --server-url; exit 3 (no_stored_token),
  listing stored keys, when none matches.
- `--wait-for-auth <sec>` — poll oauth.json (500ms) until a token for
  --server-url appears, then proceed; timeout → exit 3 (auth_wait_timeout).
- `--list-stored-auth` — print `{oauthStatePath, storedServerUrls}` and exit
  (short-circuit, no connect).
- `--print-handoff` — emit `{serverUrl, deepLink, portForwardCmd,
  oauthStatePath, apiToken, note}` for --server-url and exit.

Adaptations vs. the reference:
- State-path resolution reuses core `getStateFilePath()` (the
  MCP_INSPECTOR_OAUTH_STATE_PATH → <MCP_STORAGE_DIR>/oauth.json → default
  precedence added in #1573) instead of a CLI-local resolver.
- The state file is read through the shared isomorphic
  `parseOAuthPersistBlob`, so both the plain `{servers,idpSessions}` layout the
  web backend writes and the legacy `{state,version}` envelope are accepted.
- `parseArgs` now returns a ParseResult union so the short-circuit modes return
  without a server connection.

Blind injection: the token is passed as-is; a stale one surfaces as HTTP 401 →
exit 3. Documented in the README along with all four flags, the state-path
precedence, and a follow-up note that --print-handoff's deepLink shape is
interim pending #1576's canonical handoff format.

Tests: stored-auth.test.ts drives injection, --header coexistence, missing
--server-url, no-token exit-3, URL-normalisation matching, MCP_STORAGE_DIR
resolution, listing, handoff (+note), wait-for-auth polling/timeout, and
normalizeServerUrl units — all against a real in-process HTTP test server.
Per-file coverage ≥90 on all four dimensions (cli.ts 100% stmts/funcs/lines).

Closes #1575

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BrihGWcrM9JGRyu41nzZYw

* docs(core): scope MCP_STORAGE_DIR comment in getStateFilePath to the OAuth backend

Address review of PR #1651: the doc comment claimed MCP_STORAGE_DIR was
honoured "across the app, so setting it once points every persist backend at
the same directory", but the branch only relocates oauth.json. Narrow the
comment to state it is OAuth-backend-only (client.json/mcp.json still resolve
from getDefaultStorageDir → HOME) and record why the resolution lives here
rather than in getDefaultStorageDir (the default-path constant is evaluated at
module load, so a runtime-set MCP_STORAGE_DIR — as the CLI stored-auth /
--wait-for-auth flows set it — must be read at call time). Comment-only; no
behavior change.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BrihGWcrM9JGRyu41nzZYw

* review(cli): per-tool-tolerant app-info listing + drop dead helper (PR #1653)

Address review of PR #1653:

- collectAppInfo now never throws: a malformed `_meta.ui.resourceUri`
  (extractAppInfo throws) folds into `{hasApp:false, resourceError}` just like a
  resources/read failure. This makes `tools/list --app-info` per-tool tolerant —
  one bad tool no longer aborts the whole NDJSON listing with a generic exit-1.
  Guarding inside collectAppInfo (vs. a loop-local try/catch) keeps the branch
  unit-testable; added an emit-result.test.ts case for the malformed-URI path.
- Documented that `tools/list --app-info` always emits NDJSON regardless of
  `--format` (the per-tool list shape is fixed; --format json only reshapes the
  single-result paths) — in both the code comment and the README.
- Removed the now-unused `expectJsonError` helper (its only caller moved to the
  exit-5 tool_not_found contract).

Coverage stays ≥90 on all four dimensions (cli.ts 100% stmts/funcs/lines).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BrihGWcrM9JGRyu41nzZYw

* review(cli): stored-auth follow-ups — TODO(#1576), wait-for-auth guard test, docs (PR #1655)

Address review of PR #1655:

- Added an explicit TODO(#1576) on buildHandoff's deepLink: `transport:"http"`
  is hardcoded even for SSE, and `autoConnect=<token>` is not one of the three
  token sources the web app reads (per CLAUDE.md) — both to be reconciled with
  #1576's canonical handoff format.
- Added a test for `--wait-for-auth` without `--server-url`, covering the
  previously-untested `--wait-for-auth` arm of the shared missing-server-url
  guard's message ternary.
- Documented that `--list-stored-auth` / `--print-handoff` are mutually
  exclusive short-circuit modes (list takes precedence) and that a stored
  refresh_token is not yet used (noted as a follow-up in code + README).

No behavior change; coverage stays ≥90 on all four dimensions (cli.ts 100%
stmts/funcs/lines).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BrihGWcrM9JGRyu41nzZYw

---------

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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@ -80,6 +80,8 @@ npx @modelcontextprotocol/inspector --cli https://my-mcp-server.example.com --tr
When a server is loaded from a `--catalog`/`--config` file, its per-server settings (headers, connection/request timeouts, and OAuth) are applied to the connection — the same resolution the TUI uses. A `--header` flag overrides the file's headers for that run while leaving the file's timeouts and OAuth in place.
**Environment-variable semantics.** `MCP_CATALOG_PATH` is honored only when no ad-hoc target is given (positional command, `--server-url`, or `--transport`) — so a shell that exports it can still run one-off ad-hoc invocations without hitting the catalog/ad-hoc conflict. `MCP_STORAGE_DIR` sets the storage directory used by the OAuth persist backend (`<MCP_STORAGE_DIR>/oauth.json`); the per-file `MCP_INSPECTOR_OAUTH_STATE_PATH` override still takes precedence over it.
### HTTP proxy support
Connections to remote HTTP/SSE servers honor the conventional proxy environment variables: `HTTPS_PROXY` / `HTTP_PROXY` (and their lowercase forms) select the proxy, and `NO_PROXY` exempts hosts. This applies to the Node transport shared by the CLI and the web backend — no inspector-specific flag is needed. When a proxy variable is set, outbound requests are routed through undici's `EnvHttpProxyAgent`.
@ -96,15 +98,45 @@ Options that specify the MCP server (catalog/config file, ad-hoc command/URL, en
| Option | Description |
| ----------------------------- | ----------------------------------------------------------------------------------------- |
| `--method <method>` | MCP method to invoke (e.g. `tools/list`, `tools/call`, `resources/list`, `prompts/list`). |
| `--method <method>` | MCP method to invoke. Supports `initialize` (connect-only probe → `{serverInfo, protocolVersion, capabilities, instructions}`), `tools/list`, `tools/call`, `resources/list`, `resources/read`, `resources/templates/list`, `prompts/list`, `prompts/get`, `logging/setLevel`. |
| `--tool-name <name>` | Tool name (for `tools/call`). |
| `--tool-arg <key=value>` | Tool argument; repeat for multiple. Use `key='{"json":true}'` for JSON. |
| `--tool-arg <key=value>` | Tool argument; repeat for multiple. Use `key='{"json":true}'` for JSON. Values are coerced (JSON-parsed, so `count=1` becomes a number). |
| `--tool-args-json <json>` | Tool arguments as a single JSON object (e.g. `'{"zip":"10001"}'`). Passed verbatim — no `key=value` coercion, so `"012"` stays a string. Mutually exclusive with `--tool-arg`. |
| `--uri <uri>` | Resource URI (for `resources/read`). |
| `--prompt-name <name>` | Prompt name (for `prompts/get`). |
| `--prompt-args <key=value>` | Prompt arguments; repeat for multiple. |
| `--log-level <level>` | Logging level for `logging/setLevel` (e.g. `debug`, `info`). |
| `--metadata <key=value>` | General metadata (key=value); applied to all methods. |
| `--tool-metadata <key=value>` | Tool-specific metadata for `tools/call`. |
| `--connect-timeout <ms>` | Connection timeout in ms. Defaults to `15000` for ad-hoc `--server-url`/target runs (so a black-holed host fails fast) and to the file-level timeout for `--catalog`/`--config` runs. `0` disables the timeout. |
| `--app-info` | Probe a tool's MCP App UI metadata without invoking it. With `--method tools/call --tool-name <name>`: prints one JSON line (`hasApp`, `resourceUri`, `csp`, `permissions`, `domain`, …) and exits `0` if the tool has an app or `2` (`no_app`) if not. With `--method tools/list`: emits NDJSON — one app-info line per tool over a single connection. |
| `--format <text\|json>` | Output format. `text` (default) pretty-prints the result. `json` emits a single JSON object on stdout (`{ "result": … }`, plus `{ "appInfo": … }` as a sibling key for App tools) with no banners, so the whole output pipes cleanly into `jq`. |
#### App probing (`--app-info`) and machine-readable output (`--format json`)
`--app-info` inspects a tool's [MCP App](https://modelcontextprotocol.io) UI posture **without calling the tool**, so a pipeline can decide whether to open a browser before touching one:
```bash
# Probe one tool. Exits 0 (has app) or 2 (no_app). One JSON line on stdout.
mcp-inspector --cli <server> --method tools/call --tool-name my_tool --app-info
# → {"hasApp":true,"toolName":"my_tool","resourceUri":"ui://…","csp":{…},"permissions":{…},"prefersBorder":true,"resourceMimeType":"text/html"}
# Probe every tool at once — NDJSON, one line per tool, single connection.
mcp-inspector --cli <server> --method tools/list --app-info | jq -c 'select(.hasApp)'
```
Exit semantics: a tool that **has** an app exits `0`; one with **no** app exits `2` (`no_app`); a **missing** tool exits `5` (`tool_not_found`) — distinct so a typo isn't mistaken for "no app". A probe failure (an unreadable UI resource, or a malformed `_meta.ui.resourceUri`) is tolerated and reported in a `resourceError` field rather than aborting — so in `tools/list --app-info` one bad tool never kills the rest of the listing.
`--format json` wraps any method's output in a single stdout envelope with no banners, so App tools and plain tools both pipe cleanly into `jq`:
```bash
mcp-inspector --cli <server> --method tools/call --tool-name my_app_tool --format json
# → {"result":{…tool result…},"appInfo":{"hasApp":true,"resourceUri":"ui://…",…}}
```
> `tools/list --app-info` always emits NDJSON (one raw app-info object per line) **regardless of `--format`** — the per-tool list shape is fixed. `--format json` only reshapes the single-result paths (`tools/call`, `tools/list` without `--app-info`, etc.) into the `{result[, appInfo]}` envelope.
A `tools/call` that returns `isError:true` still prints its payload but exits `5` (`tool_is_error`) so `&&` chains don't proceed on a failed call.
### CLI-specific (OAuth for HTTP servers)
@ -155,6 +187,34 @@ npx @modelcontextprotocol/inspector --cli --catalog mcp.json --server my-http-se
See [EMA / enterprise-managed auth](../../specification/v2_auth_ema.md) and [OAuth smoke testing](../../specification/v2_auth_smoke_testing.md) (§3 Stytch/CIMD; [§5 mid-session manual validation](../../specification/v2_auth_smoke_testing.md#5-mid-session-auth--step-up--manual-validation) — CLI **C1–C2**).
#### Stored-auth (web → CLI handoff)
For the common case where OAuth was already completed in the **web inspector on the same machine**, the CLI can reuse the resulting token instead of running its own interactive flow. It reads the shared OAuth state file (the `oauth.json` the web backend writes) directly from disk and injects `Authorization: Bearer <token>` for `--server-url`.
| Option | Description |
| ----------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `--use-stored-auth` | Read the stored access token for `--server-url` and inject it as `Authorization: Bearer`. Exits `3` (`no_stored_token`) — listing the stored keys — when no token matches. Requires `--server-url`. |
| `--wait-for-auth <sec>` | Poll the OAuth state file (500 ms interval) until a token for `--server-url` appears, then proceed as if `--use-stored-auth` were set. Times out at `<sec>` with exit `3` (`auth_wait_timeout`). Use after handing off to a human to complete OAuth in a browser. |
| `--list-stored-auth` | Print `{ oauthStatePath, storedServerUrls }` (the server keys that currently have a token) and exit. No server connection is made. |
| `--print-handoff` | Print a JSON handoff block (`deepLink`, `portForwardCmd`, `oauthStatePath`, `apiToken`) for `--server-url` and exit — everything a script/remote VM needs to drive the browser-side OAuth dance. Requires `--server-url`. |
**State-file resolution** follows `MCP_INSPECTOR_OAUTH_STATE_PATH` → `<MCP_STORAGE_DIR>/oauth.json` → `~/.mcp-inspector/storage/oauth.json` — the same precedence the rest of the Inspector uses, so the CLI and web backend agree on the file. Server keys are canonicalised with `new URL().href` (the scheme the web store writes), so a trailing-slash or case mismatch between the URL a human opened and the one the agent passed still resolves.
**Blind injection.** The token is injected as-is; the CLI does not validate or refresh it (a stored `refresh_token` is not yet used — a natural follow-up). A stale/expired access token surfaces as an HTTP `401` on the first request → exit `3` (`auth_required`). Re-complete the flow in the web inspector (or use `--wait-for-auth`) and retry.
**Short-circuit modes.** `--list-stored-auth` and `--print-handoff` each print their output and exit without connecting to a server; they ignore the method/target flags. They are mutually exclusive — if both are passed, `--list-stored-auth` takes precedence.
> The `deepLink` shape emitted by `--print-handoff` is interim, pending the web deep-link auto-connect work ([#1576](https://github.com/modelcontextprotocol/inspector/issues/1576)); it will be reconciled with that issue's canonical handoff format once it lands.
```bash
# On a remote VM: print what a human needs to complete OAuth in their browser.
mcp-inspector --cli --server-url https://api.example/mcp --print-handoff
# Then block until the token lands and run the call with it.
mcp-inspector --cli --transport http --server-url https://api.example/mcp \
--wait-for-auth 120 --method tools/list
```
## Exit codes & error envelopes
Every non-zero exit maps to a stable failure class, so a programmatic caller