feat(integrations): support SPECIFY_<KEY>_EXTRA_ARGS env var for agent subprocess flags (#2596)

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

Read a per-integration env var (SPECIFY_<KEY>_EXTRA_ARGS) inside
`SkillsIntegration.build_exec_args`, `MarkdownIntegration.build_exec_args`,
and `TomlIntegration.build_exec_args` and append the parsed flags to the
spawned agent's argv, gated per integration key.

Operators can now opt into extra CLI flags (e.g.
`SPECIFY_CLAUDE_EXTRA_ARGS=--dangerously-skip-permissions`) without
modifying any SKILL or workflow YAML. Useful in CI / non-interactive
contexts where the spawned `<agent> -p ...` would otherwise hang on
an internal permission or input prompt invisible to the parent
`specify workflow run` process.

Key normalization: `kiro-cli` → `SPECIFY_KIRO_CLI_EXTRA_ARGS` (hyphen
replaced with underscore, then uppercased).

Default (env var unset or whitespace-only) is byte-identical to
previous behaviour. Extra args are inserted between `-p prompt` and
the model / output-format flags so they cannot clobber canonical
Spec Kit args.

Implementation: a single helper `IntegrationBase._apply_extra_args_env_var`
encapsulates the env-var read + shlex parsing; each of the three
concrete `build_exec_args` implementations calls it.

Closes #2595

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix(integrations): wire SPECIFY_<KEY>_EXTRA_ARGS into Codex/Devin/Opencode/Copilot

Four integrations override `build_exec_args` and were silently
ignoring the env-var hook introduced in the previous commit:

- CodexIntegration (`codex exec ...`)
- DevinIntegration (`devin -p ...`)
- OpencodeIntegration (`opencode run ...`)
- CopilotIntegration (`copilot -p ...`)

Each now calls `self._apply_extra_args_env_var(args)` between the
base argv and the canonical Spec Kit flags (matching the placement
in `MarkdownIntegration`, `TomlIntegration`, and `SkillsIntegration`),
so operator-injected flags cannot clobber `--model` / `--output-format`
/ `--json`.

Adds 4 parameterized override-integration tests locking the wiring
per agent. Also cleans up an inline `__import__("os").environ` in the
fixture to a top-of-file `import os`.

Drive-by typing fix: guard `self.registrar_config.get(...)` in
`CopilotIntegration.add_commands` against the `None` case, matching
the pattern already used in `base.py` for the same access.

Addresses Copilot review on #2596.

* fix(integrations): apply Opencode extra-args before prompt-derived --command

When the Opencode prompt starts with `/`, `build_exec_args` injects
`--command <X>` derived from the prompt. The previous placement of
`self._apply_extra_args_env_var(args)` appended operator-injected
args AFTER that `--command`, so a user setting
`SPECIFY_OPENCODE_EXTRA_ARGS="--command override"` could redirect the
command under typical last-wins repeated-flag CLI semantics.

Move the hook to immediately after `args = [self.key, "run"]`, before
the prompt-parsing block. The operator's `--command override` (if
any) now precedes the Spec Kit-derived `--command speckit`, so the
canonical choice wins.

Adds `test_opencode_extra_args_cannot_clobber_prompt_derived_command`
locking the ordering. Also corrects the module docstring to describe
the hook as living in `IntegrationBase` (not `SkillsIntegration`) and
to acknowledge that this file covers Codex/Devin/Opencode/Copilot in
addition to SkillsIntegration stubs.

Addresses Copilot review on #2596.

* fix(integrations): honour SPECIFY_COPILOT_EXTRA_ARGS in dispatch_command

`CopilotIntegration` is the only integration that overrides
`dispatch_command` — it builds `cli_args` inline rather than going
through `build_exec_args`. The previous commit wired
`_apply_extra_args_env_var` into `build_exec_args` but workflow
execution calls `dispatch_command`, so `SPECIFY_COPILOT_EXTRA_ARGS`
was silently ignored at runtime.

Add the hook in `dispatch_command` immediately after
`cli_args = ["copilot", "-p", prompt]`, mirroring the placement in
`build_exec_args` (between `-p prompt` and the canonical
`--agent` / `--yolo` / `--model` / `--output-format` flags).

`IntegrationBase.dispatch_command` already delegates to
`build_exec_args`, so Codex, Devin, and Opencode continue to honour
their respective env vars through inheritance — no further changes
needed for them.

Adds two end-to-end tests that monkeypatch `subprocess.run` and
assert the env-var args reach the executed argv:
- `test_copilot_dispatch_command_includes_extra_args` locks the
  bypass fix on the overridden path.
- `test_codex_dispatch_command_includes_extra_args` locks the
  inherited-base-dispatch path for the other three integrations.

Addresses Copilot review on #2596.

* refactor(integrations): rename env var to SPECIFY_INTEGRATION_<KEY>_EXTRA_ARGS

Per maintainer request: scope the operator-injected env var to the
integration subsystem by prepending `INTEGRATION_` to the key
segment, so it does not collide with other Spec Kit env-var
namespaces.

Renames everywhere it appears:
- Helper `IntegrationBase._apply_extra_args_env_var` env_name
  format and docstring (`base.py`).
- Inline comment in `CopilotIntegration.dispatch_command`.
- All `monkeypatch.setenv(...)` calls, docstrings, and the
  autouse fixture's scope filter in
  `tests/integrations/test_extra_args.py`.

No behaviour change beyond the variable name. Default (env var
unset) still byte-identical to before this PR.

Addresses review on #2596.

* fix(integrations): raise actionable error on malformed EXTRA_ARGS quoting

Wrap `shlex.split` in `_apply_extra_args_env_var` so an unmatched quote
in `SPECIFY_INTEGRATION_<KEY>_EXTRA_ARGS` surfaces a clear `ValueError`
naming the offending env var and showing the invalid value, instead of
crashing workflow dispatch with a bare shlex traceback. Adds a new test
locking the actionable error path.

Addresses Copilot review feedback on #2596.

* test(integrations): use `_copilot_executable()` in Copilot extra-args test

`test_copilot_integration_honours_extra_args` hardcoded `"copilot"`
in the expected argv, but `CopilotIntegration.build_exec_args` calls
`_copilot_executable()` which returns `"copilot.cmd"` on Windows
(`os.name == "nt"`). The test passed on Linux/macOS and failed on
all three Windows-latest matrix entries.

Resolve by importing `_copilot_executable` alongside `CopilotIntegration`
and using it as the first expected argv token. The companion
`test_copilot_dispatch_command_includes_extra_args` already uses
`index()` lookups rather than full-argv equality so it was unaffected.

* fix(integrations): couple Codex executable to self.key + cover base classes

Two Copilot findings on the latest pass:

1. `CodexIntegration.build_exec_args` hardcoded the executable name
   as the literal `"codex"` while the env-var lookup derives from
   `self.key`. The two should stay coupled (matching Devin/Opencode,
   which both use `self.key` already). Replace the literal with
   `self.key` so the argv and env-var scoping cannot drift.

2. `tests/integrations/test_extra_args.py` covered the
   `SkillsIntegration` mechanism (via stubs near the top) and the
   four `build_exec_args` overrides (Codex/Devin/Opencode/Copilot)
   end-to-end, but did not exercise the `MarkdownIntegration` or
   `TomlIntegration` base implementations directly. Add bare
   `_MarkdownAgentStub` and `_TomlAgentStub` test stubs and a test
   each — the most common integration pattern (Amp, Auggie, Generic,
   Gemini, Tabnine, …) inherits without overriding, so the base
   wiring is now locked.

Full suite: 3011 passed (was 3009), 40 skipped, no regressions.

Addresses Copilot review feedback on #2596.

* fix(integrations): rename env var to SPECKIT_INTEGRATION_<KEY>_EXTRA_ARGS

Renames the env-var hook prefix from `SPECIFY_INTEGRATION_*` to
`SPECKIT_INTEGRATION_*` to match the established codebase
convention for integration-subsystem env vars
(`SPECKIT_INTEGRATION_CATALOG_URL` in `integrations/catalog.py`,
`SPECKIT_COPILOT_ALLOW_ALL_TOOLS` in `integrations/copilot/__init__.py`).

The `SPECIFY_*` prefix is reserved for user-facing
feature-resolution variables (`SPECIFY_FEATURE`,
`SPECIFY_FEATURE_DIRECTORY`); reusing it for integration-subsystem
scoping would introduce a second integration namespace under a
different prefix, confusing operators who already set
`SPECKIT_INTEGRATION_CATALOG_URL`.

Also reverts the unrelated defensive `arg_placeholder` /
`registrar_config is None` guard in
`CopilotIntegration.setup_skills_mode` — it was a drive-by pyright
cleanup mixed into this PR. Every concrete integration sets
`registrar_config` so the guard never fires in practice; the
typing issue belongs in a focused follow-up rather than this
env-var-hook PR.

Updates everywhere the old prefix appeared:
- `IntegrationBase._apply_extra_args_env_var` helper + docstring
- `CopilotIntegration.dispatch_command` inline comment
- All `monkeypatch.setenv(...)` calls in `tests/integrations/test_extra_args.py`
- The autouse fixture scope filter
- Test module docstring

Full suite: 3011 passed, 40 skipped, no regressions.

Addresses Copilot review feedback on #2596.

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: doquanghuy

src/specify_cli/integrations/base.py

@@ -13,7 +13,9 @@
 
 from __future__ import annotations
 
+import os
 import re
+import shlex
 import shutil
 from abc import ABC
 from dataclasses import dataclass
@@ -144,6 +146,43 @@ def build_exec_args(
         """
         return None
 
+    def _apply_extra_args_env_var(self, args: list[str]) -> None:
+        """Append `SPECKIT_INTEGRATION_<KEY>_EXTRA_ARGS` env-var value to *args*.
+
+        Operators can inject extra CLI flags into the spawned agent
+        subprocess by setting an env var named for the integration key,
+        e.g. `SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS="--dangerously-skip-permissions"`.
+        The `INTEGRATION` segment scopes the variable to this subsystem
+        so it does not collide with other Spec Kit env-var namespaces.
+        Hyphens in the integration key are replaced with underscores
+        and the key is uppercased
+        (e.g. `kiro-cli` → `SPECKIT_INTEGRATION_KIRO_CLI_EXTRA_ARGS`).
+
+        Useful in CI / non-interactive contexts where the spawned agent
+        needs flags that change its prompt-handling behaviour.
+        Default behaviour (env var unset or whitespace-only) is a no-op
+        — *args* is unchanged. Multi-token values are parsed via
+        `shlex.split`.
+
+        See issue #2595.
+        """
+        env_name = (
+            f"SPECKIT_INTEGRATION_{self.key.upper().replace('-', '_')}_EXTRA_ARGS"
+        )
+        extra = os.environ.get(env_name, "").strip()
+        if not extra:
+            return
+        try:
+            tokens = shlex.split(extra)
+        except ValueError as exc:
+            raise ValueError(
+                f"{env_name} is not parseable as a POSIX-quoted command line "
+                f"(value: {extra!r}). shlex reported: {exc}. "
+                f"Use single or double quotes to group multi-word values, e.g. "
+                f'{env_name}=\'--flag "value with spaces"\'.'
+            ) from exc
+        args.extend(tokens)
+
     def build_command_invocation(self, command_name: str, args: str = "") -> str:
         """Build the native slash-command invocation for a Spec Kit command.
 
@@ -857,6 +896,7 @@ def build_exec_args(
         if not self.config or not self.config.get("requires_cli"):
             return None
         args = [self.key, "-p", prompt]
+        self._apply_extra_args_env_var(args)
         if model:
             args.extend(["--model", model])
         if output_json:
@@ -944,6 +984,7 @@ def build_exec_args(
         if not self.config or not self.config.get("requires_cli"):
             return None
         args = [self.key, "-p", prompt]
+        self._apply_extra_args_env_var(args)
         if model:
             args.extend(["-m", model])
         if output_json:
@@ -1362,6 +1403,7 @@ def build_exec_args(
         if not self.config or not self.config.get("requires_cli"):
             return None
         args = [self.key, "-p", prompt]
+        self._apply_extra_args_env_var(args)
         if model:
             args.extend(["--model", model])
         if output_json:

src/specify_cli/integrations/codex/__init__.py

@@ -37,7 +37,12 @@ def build_exec_args(
         output_json: bool = True,
     ) -> list[str] | None:
         # Codex uses ``codex exec "prompt"`` for non-interactive mode.
-        args: list[str] = ["codex", "exec", prompt]
+        # Use ``self.key`` so the executable name stays coupled to the
+        # env-var lookup (which also derives from ``self.key``), matching
+        # the pattern in Devin/Opencode and avoiding drift if the key
+        # ever changes.
+        args: list[str] = [self.key, "exec", prompt]
+        self._apply_extra_args_env_var(args)
         if model:
             args.extend(["--model", model])
         if output_json:

src/specify_cli/integrations/copilot/__init__.py

@@ -149,6 +149,7 @@ def build_exec_args(
         # (default: enabled).  The deprecated SPECKIT_ALLOW_ALL_TOOLS
         # is also honoured as a fallback.
         args = [_copilot_executable(), "-p", prompt]
+        self._apply_extra_args_env_var(args)
         if _allow_all():
             args.append("--yolo")
         if model:
@@ -217,6 +218,11 @@ def dispatch_command(
             prompt = args or ""
 
         cli_args = [_copilot_executable(), "-p", prompt]
+        # Honour SPECKIT_INTEGRATION_COPILOT_EXTRA_ARGS for real workflow
+        # runs.  `dispatch_command` builds cli_args inline rather than
+        # going through `build_exec_args`, so the hook must be invoked
+        # here too — otherwise the env var is silently ignored.
+        self._apply_extra_args_env_var(cli_args)
         if not skills_mode:
             cli_args.extend(["--agent", agent_name])
         if _allow_all():

src/specify_cli/integrations/devin/__init__.py

@@ -49,6 +49,7 @@ def build_exec_args(
         kept on the integration for tool detection.
         """
         args = [self.key, "-p", prompt]
+        self._apply_extra_args_env_var(args)
         if model:
             args.extend(["--model", model])
         return args

src/specify_cli/integrations/opencode/__init__.py

@@ -29,6 +29,11 @@ def build_exec_args(
         output_json: bool = True,
     ) -> list[str] | None:
         args = [self.key, "run"]
+        # Apply operator-injected extra args before the prompt-derived
+        # --command and the canonical --format/-m flags so Spec Kit's
+        # later appends remain authoritative under repeated-flag CLI
+        # semantics.
+        self._apply_extra_args_env_var(args)
 
         message = prompt
         if prompt.startswith("/"):