docs: separate the API-only flags from the ones needing a checkout

Two flags in the reference said one thing and did another.

`-o` was listed as a global output-format flag and the Tips section
recommended `-o json` without qualification. On `tea api` it is a file
name: `-o json` writes the body to a file called json and leaves stdout
empty, so the next parse fails with a JSONDecodeError that looks like a
server refusal. Scoped to entity commands, and api's meaning named in
all three places that mention it.

`--repo owner/repo` was documented as a general substitute for standing
in a checkout. For `pulls create`, `pulls checkout` and `pulls clean` it
is not: the slug is rejected with 'local repository required', advice
that reads like the flag was missing. Verified from outside any repo —
those three refuse a slug and accept a path, while pulls list,
milestones, releases and times take the slug from anywhere. All three
working forms are written down, including the git-worktree one (point
--repo at the main checkout) and the api fallback.

Closes #35
Closes #28

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

skills/use/references/tea/helpers.md

@@ -26,5 +26,5 @@ Authenticated HTTP request to the Gitea API. Endpoints are auto-prefixed with `/
 - `--data/-d` — raw JSON body (`@file` / `@-`). Incompatible with `-f`/`-F`.
 - `--header/-H key:value` (repeatable)
 - `--include/-i` — write status + response headers to stderr.
-- `--output/-o <file>` — write response body to file (`-` = stdout).
+- `--output/-o <file>` — write response body to file (`-` = stdout). **Not the entity commands' format flag**: `-o json` here creates a file named `json` and prints nothing. The body is already JSON.
 - Quote the endpoint if it contains `?` or `&` to prevent shell expansion.