@@ -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("/"):
@@ -37,7 +42,6 @@ def build_exec_args(
                 args.extend(["--command", command])
                 message = remainder
 
-        self._apply_extra_args_env_var(args)
         if model:
             args.extend(["-m", model])
         if output_json:
 
@@ -1,5 +1,12 @@
-"""Tests for the per-integration `SPECIFY_<KEY>_EXTRA_ARGS` env-var hook
-in `SkillsIntegration.build_exec_args`. See issue #2595."""
+"""Tests for the per-integration `SPECIFY_<KEY>_EXTRA_ARGS` env-var hook.
+
+The hook is implemented in `IntegrationBase._apply_extra_args_env_var`
+and wired into every concrete `build_exec_args` —
+`MarkdownIntegration`, `TomlIntegration`, `SkillsIntegration`, plus the
+overrides in Codex, Devin, Opencode and Copilot. These tests cover both
+the shared mechanism (via `SkillsIntegration` stubs near the top of the
+file) and each override integration end-to-end (further down). See
+issue #2595."""
 
 import os
 
@@ -216,6 +223,39 @@ def test_opencode_integration_honours_extra_args(monkeypatch):
     ]
 
 
+def test_opencode_extra_args_cannot_clobber_prompt_derived_command(
+    monkeypatch,
+):
+    """Operator-injected extra args must appear BEFORE the prompt-derived
+    ``--command <X>`` so that Spec Kit's command selection wins under
+    repeated-flag CLI semantics (last value typically takes precedence).
+
+    Locks against the regression where an operator setting
+    ``SPECIFY_OPENCODE_EXTRA_ARGS="--command malicious"`` could redirect
+    a slash-prefixed prompt to a different command.
+    """
+    from specify_cli.integrations.opencode import OpencodeIntegration
+
+    monkeypatch.setenv(
+        "SPECIFY_OPENCODE_EXTRA_ARGS", "--command operator-override"
+    )
+    args = OpencodeIntegration().build_exec_args("/speckit body text")
+    # Prompt-derived "--command speckit" appears AFTER the
+    # operator-injected one, so a CLI that resolves repeated flags
+    # last-wins will honour Spec Kit's choice.
+    assert args == [
+        "opencode",
+        "run",
+        "--command",
+        "operator-override",
+        "--command",
+        "speckit",
+        "--format",
+        "json",
+        "body text",
+    ]
+
+
 def test_copilot_integration_honours_extra_args(monkeypatch):
     from specify_cli.integrations.copilot import CopilotIntegration