Fix --inputs-file: inputs from a JSON file or stdin never reach the objective

[rr-aniket-wankhede]

The bug

--inputs-file is documented in DESIGN.md but was never implemented. The run
command parses its extra args as declared-input flags, so the token was consumed
as an input named inputs_file whose value was the path. The real inputs never
arrived, and the task failed before the model was invoked.

Root cause: charter/cli.py in run(): the flag loop (key = token[2:].replace("-", "_") → context[key] = _typed(value)) has no special case for --inputs-file, so the flag-path and file-path never converge on the same invoke context.

Repro

printf '{"ticket_id": "4821"}' > /tmp/inputs.json
charter run input-file-repro --inputs-file /tmp/inputs.json
# ACTUAL:   task starts, then fails:
#           "ticket_id was not given, and the objective needs it. Run: ..."
#           llm_calls: 0  (model never invoked — empty invoke context)
# EXPECTED: same as the flag path:
charter run input-file-repro --ticket_id 4821   # completes, llm_calls: 1

Agent config used:

apiVersion: charter/v1
kind: AgentConfig
name: input-file-repro
version: 1
model: <any model on your provider>
objective: |
  Report the ticket id {{ inputs.ticket_id }}.
inputs:
  ticket_id: { type: string, required: true }
response_format:
  answer:
    type: string
    description: The ticket id.

The fix

run() now recognises --inputs-file (space, =, and - for stdin) and merges
the parsed JSON object into the same invoke_workflow(context=...) the flags
build (_read_inputs). A file that is missing, unparsable, or not a JSON object
is refused locally with a clear error, without submitting a request.

While testing this, the = form exposed a latent parser bug that the fix also
corrects: the loop replaced - with _ across the whole token before splitting
on =, so any --flag=value-with-dashes was silently mangled (--inputs-file=/some-path
became /some_path). The split now happens first, so only the flag name is normalized.

Tests

• Unit (tests/test_cli.py::TestRunInputsFile): the CLI path with a file,
  stdin -, the = form mixed with flags, and local refusal of bad files
  all asserting the exact context handed to invoke_workflow.
• E2E (tests/e2e/test_inputs_file.py): the real charter run command in a
  subprocess, against a real control plane and store, with a scripted model that
  asserts the objective the model is handed contains the rendered value, the
  structured result, and total_llm_calls == 1 (the bug showed 0).

Full suites pass: 345 unit tests, 31 e2e (4 skipped: no live providers locally).