feat(integrations): generalize post-processing to all format types (#3311)

* feat(integrations): add post_process_command_content() hook for all format types

Add post_process_command_content(self, content: str) -> str to IntegrationBase
with a no-op default. Wire it into register_commands() for non-skills format
types (Markdown, TOML, YAML) after format rendering, before writing to disk.
Also applies to aliases rendered via the inject_name path (cline, forge).

Skills-format agents are excluded to preserve the existing
post_process_skill_content() path and avoid double-processing.

This gives extension authors a clean per-agent content transformation seam
for all 21 non-skills integrations that previously had no post-processing hook.

Ref: #3303

Assisted-By: 🤖 Claude Code

* fix: initialize _integration before conditional branch

Prevents potential UnboundLocalError if the non-skills guard is
refactored without updating the alias path reference.

Assisted-By: 🤖 Claude Code

src/specify_cli/agents.py

@@ -706,6 +706,17 @@ class CommandRegistrar:
             else:
                 raise ValueError(f"Unsupported format: {agent_config['format']}")
 
+            # -- Post-process for non-skills agents -----------------------
+            _integration = None
+            if agent_config["extension"] != "/SKILL.md":
+                from specify_cli.integrations import (  # noqa: PLC0415
+                    get_integration,
+                )
+
+                _integration = get_integration(agent_name)
+                if _integration is not None:
+                    output = _integration.post_process_command_content(output)
+
             dest_file = commands_dir / f"{output_name}{agent_config['extension']}"
             self._ensure_inside(dest_file, commands_dir)
             dest_file.parent.mkdir(parents=True, exist_ok=True)
@@ -766,6 +777,9 @@ class CommandRegistrar:
                         raise ValueError(
                             f"Unsupported format: {agent_config['format']}"
                         )
+
+                    if agent_config["extension"] != "/SKILL.md" and _integration is not None:
+                        alias_output = _integration.post_process_command_content(alias_output)
                 else:
                     # For other agents, reuse the primary output
                     alias_output = output

src/specify_cli/integrations/base.py

@@ -123,6 +123,19 @@ class IntegrationBase(ABC):
     integration that sets this flag.
     """
 
+    def post_process_command_content(self, content: str) -> str:
+        """Transform command content after format rendering.
+
+        Called by ``register_commands()`` for non-skills format types
+        (Markdown, TOML, YAML) after the command has been rendered into
+        its target format and before writing to disk.  Skills-format
+        agents use ``post_process_skill_content()`` instead.
+
+        Subclasses may override to inject agent-specific content.
+        The default implementation returns *content* unchanged.
+        """
+        return content
+
     # -- Public API -------------------------------------------------------
 
     @classmethod