ci: Replace ARM failure management with skip marker system

- Removed scripts for managing ARM build failures and filtering tests.
- Introduced `filter_arm_tests.py` to skip ARM tests based on `.skip-arm` marker files.
- Updated GitHub Actions workflows to utilize the new skip marker system.
- Revised documentation to reflect changes in ARM test management.

Author: edmundmiller

.github/scripts/filter_arm_failure_tests.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+"""Skip ARM tests for modules with .skip-arm marker files"""
+import json, sys, os
+
+def main():
+    if len(sys.argv) != 2:
+        print(json.dumps([]))
+        return
+
+    paths = json.loads(sys.argv[1])
+    filtered = []
+
+    for path in paths:
+        # Extract module dir (modules/nf-core/xxx or subworkflows/nf-core/xxx)
+        parts = path.split("/")
+        if len(parts) >= 3 and parts[1] == "nf-core":
+            module_dir = "/".join(parts[:3])
+            if os.path.exists(f"{module_dir}/.skip-arm"):
+                print(f"⚠️  Skipping ARM tests for {path}", file=sys.stderr)
+                continue
+        filtered.append(path)
+
+    print(json.dumps(filtered))
+
+if __name__ == "__main__": main()