feat(integrations): support SPECIFY_<KEY>_EXTRA_ARGS env var for agent subprocess flags

[doquanghuy]

Description

Closes #2595.

Adds a per-integration env-var hook
(SPECIFY_<KEY>_EXTRA_ARGS) so operators can inject extra CLI
flags into the spawned agent subprocess without modifying any
SKILL or workflow YAML. The motivating use case is non-interactive
contexts (CI, batch, sandboxed eval) where the spawned
<agent> -p ... hangs silently on an internal permission or
input prompt invisible to the parent specify workflow run
process.

What changed

• New helper IntegrationBase._apply_extra_args_env_var(args) —
  reads SPECIFY_<KEY>_EXTRA_ARGS from env (key normalized: -
  → _, uppercased), parses with shlex.split, and appends to
  args. No-op when the env var is unset or whitespace-only.
• MarkdownIntegration.build_exec_args,
  TomlIntegration.build_exec_args, and
  SkillsIntegration.build_exec_args each call the helper between
  args = [self.key, "-p", prompt] and the model / output-format
  appends — so extra args sit between -p prompt and the
  canonical Spec Kit flags and cannot clobber them.
• New tests/integrations/test_extra_args.py with 7 tests
  covering: default no-op, single-token, multi-token via shlex,
  whitespace-only treated as unset, other-integration env var
  ignored (per-key scoping), key normalization
  (kiro-cli → KIRO_CLI), requires_cli: False
  short-circuit.

Default behaviour preserved

When SPECIFY_<KEY>_EXTRA_ARGS is unset for the active
integration, build_exec_args returns byte-identical argv to
before this change. Existing operators see no difference.

Examples

# Non-interactive Claude run in CI
SPECIFY_CLAUDE_EXTRA_ARGS="--dangerously-skip-permissions" \
    specify workflow run my-pipeline

# Per-integration scoping
SPECIFY_GEMINI_EXTRA_ARGS="--max-turns 3" specify workflow run …

# Multi-token via shlex
SPECIFY_CLAUDE_EXTRA_ARGS="--dangerously-skip-permissions --max-turns 3" …

# Hyphenated keys
SPECIFY_KIRO_CLI_EXTRA_ARGS="--some-flag" specify workflow run …

Testing

• Tested locally with uv run specify --help
• Ran existing tests: pytest tests/ -q →
  2943 passed, 35 skipped (was 2936 before; +7 new tests
  added in this PR).
• Tested with a sample project: invoked specify workflow run
  against a Claude command step with
  SPECIFY_CLAUDE_EXTRA_ARGS=--dangerously-skip-permissions
  set — flag reaches the spawned claude -p ... subprocess
  and the run completes non-interactively. Same workflow
  without the env var still hangs as before (consistent with
  the pre-PR behaviour).

Manual test results

Agent: Claude Code (CLI) | OS/Shell: macOS 14 / zsh

Test	Result	Notes
Env var set → flag in argv	PASS	--dangerously-skip-permissions appears between -p prompt and --model
Env var unset → byte-identical argv	PASS	argv matches pre-PR shape exactly
Other-integration env var ignored	PASS	SPECIFY_GEMINI_EXTRA_ARGS=... does not affect Claude argv
Multi-token via shlex	PASS	"--flag-a --flag-b 3" splits into 3 tokens
Whitespace-only treated as unset	PASS	" " → no-op
Key normalization kiro-cli → KIRO_CLI	PASS	env var SPECIFY_KIRO_CLI_EXTRA_ARGS correctly read
requires_cli: False short-circuit	PASS	build_exec_args returns None; env-var hook never reached

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (described below)

Used Claude Opus to draft the implementation (env-var hook +
helper extraction), the test suite, the issue body for #2595, and
this PR body. The reproducer scenario (non-interactive claude -p
hang on permission prompts) was a real-world problem encountered
in operator practice. Code, tests, and design decisions were
human-reviewed before submission.