fix(apply): reads files within nested directories

The apply command does not read nested directories well and hence, it is
not possible to break down manifests into sub-directories and apply them
by just passing the root directory as the input along with values and
secrets. The traversal does happen while the files are processed,
however the final list of files ends up with directories which cannot be
processed during the apply phase.

This commit filters out all the files and returns them omitting any
directories.

riocli/apply/util.py

@@ -1,4 +1,4 @@
-# Copyright 2022 Rapyuta Robotics
+# Copyright 2023 Rapyuta Robotics
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -16,31 +16,34 @@
 import os
 
 
-def parse_varidac_pathargs(pathItem):
+def parse_variadic_path_args(path_item):
     glob_files = []
-    abs_path = os.path.abspath(pathItem)
-    # make it absolte
+    abs_path = os.path.abspath(path_item)
+    # make it absolute
     # does the path exist.
     #     is it a dir?  scan recursively
-    #     not a dir but has  special charaters in it?  [*?^!]
-    #        assume its a valid glob, use it to glob recursively
+    #     not a dir but has  special characters in it?  [*?^!]
+    #        assume it's a valid glob, use it to glob recursively
     #      if all else fails
     #        consider it a file path directly.
-    if os.path.exists(abs_path):
-        if os.path.isdir(abs_path):
-            # TODO: Should we keep this recursive?
-            glob_files = glob.glob(abs_path + "/**/*", recursive=True)
-        else:
-            glob_files = glob.glob(abs_path, recursive=True)
-    return glob_files
+    if not os.path.exists(abs_path):
+        return glob_files
+
+    if os.path.isdir(abs_path):
+        # TODO: Should we keep this recursive?
+        return glob.glob(abs_path + "/**/*", recursive=True)
+
+    return glob.glob(abs_path, recursive=True)
 
 
 def process_files_values_secrets(files, values, secrets):
     glob_files = []
 
-    for pathItem in files:
-        path_glob = parse_varidac_pathargs(pathItem)
-        glob_files.extend(path_glob)
+    for path_item in files:
+        path_glob = parse_variadic_path_args(path_item)
+        glob_files.extend([
+            f for f in path_glob if os.path.isfile(f)
+        ])
 
     abs_values = values
     if values and values != "":