Remove deprecated parameters

Those paremeters are deprected for over 4 years now. I found no usages
while searching for output_manifest in source.chromium.org.

R=machenbach@google.com

Bug: 1289274
Change-Id: I7d8f8ee29fdb046b255c96ad26f8dc7129b1f83a
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/tools/depot_tools/+/3402741
Auto-Submit: Josip Sokcevic <sokcevic@google.com>
Reviewed-by: Michael Achenbach <machenbach@chromium.org>
Commit-Queue: Michael Achenbach <machenbach@chromium.org>

recipes/recipe_modules/bot_update/resources/bot_update.py

@@ -923,8 +923,6 @@ def parse_args():
 
   parse.add_option('--experiments',
                    help='Comma separated list of experiments to enable')
-  parse.add_option('--root', dest='patch_root',
-                   help='DEPRECATED: Use --patch_root.')
   parse.add_option('--patch_root', help='Directory to patch on top of.')
   parse.add_option('--patch_ref', dest='patch_refs', action='append', default=[],
                    help='Git repository & ref to apply, as REPO@REF.')
@@ -955,9 +953,6 @@ def parse_args():
             'solution revision passed in already exists in the current '
             'git cache.'))
 
-  # TODO(machenbach): Remove the flag when all uses have been removed.
-  parse.add_option('--output_manifest', action='store_true',
-                   help=('Deprecated.'))
   parse.add_option('--clobber', action='store_true',
                    help='Delete checkout first, always')
   parse.add_option('--output_json',