Cleans up permissions a lot and adds missing permissions to plugin.yml

Removes the checking of both parent and child by adding the child permissions to plugin.yml
Cleans comments in the PermissionHelper class
Renames hasPermDeep to hasPermissionImplicit as I finally understand how it's supposed to work
Adds missing unmock() to prevent test errors
Adds a ton of permissions which were mentioned in the code, but did not exist in the plugin.yml

src/main/java/net/knarcraft/stargate/utility/FileHelper.java

@@ -25,10 +25,13 @@ public final class FileHelper {
     }
 
     /**
-     * Gets a buffered reader from a string pointing to a file
+     * Gets an input stream from a string pointing to an internal file
+     * 
+     * <p>This is used for getting an input stream for reading a file contained within the compiled .jar file. The file
+     * should be in the resources directory, and the file path should start with a forward slash ("/") character.</p>
      *
      * @param file <p>The file to read</p>
-     * @return <p>A buffered reader reading the file</p>
+     * @return <p>An input stream for the file</p>
      */
     public static InputStream getInputStreamForInternalFile(String file) {
         return FileHelper.class.getResourceAsStream(file);
@@ -47,10 +50,10 @@ public final class FileHelper {
     }
 
     /**
-     * Gets a buffered reader from an input stream
+     * Gets a buffered reader given an input stream
      *
      * @param inputStream <p>The input stream to read</p>
-     * @return <p>A buffered reader reading the stream</p>
+     * @return <p>A buffered reader reading the input stream</p>
      */
     public static BufferedReader getBufferedReaderFromInputStream(InputStream inputStream) {
         InputStreamReader inputStreamReader = new InputStreamReader(inputStream, StandardCharsets.UTF_8);
@@ -71,20 +74,19 @@ public final class FileHelper {
     }
 
     /**
-     * Reads key value pairs from an input stream
+     * Reads key/value pairs from an input stream
      *
      * @param bufferedReader <p>The buffered reader to read</p>
      * @return <p>A map containing the read pairs</p>
      * @throws IOException <p>If unable to read from the stream</p>
      */
     public static Map<String, String> readKeyValuePairs(BufferedReader bufferedReader) throws IOException {
-
         Map<String, String> readPairs = new HashMap<>();
 
         String line = bufferedReader.readLine();
         boolean firstLine = true;
         while (line != null) {
-            // Strip UTF BOM
+            //Strip UTF BOM from the first line
             if (firstLine) {
                 line = removeUTF8BOM(line);
                 firstLine = false;