When updating manifest from a non-checkout put changes into local_changes section.

Instead of overwriting manifest entries when updating against a local copy (not clone) of
the tests, put differences into the local_changes section, rather than overwriting the
data about upstream. This makes resyncing changes with upstream easier.
fixup! When updating manifest from a non-checkout put changes into local_changes section.
Merge pull request #1446 from w3c/jgraham/manifest_local_changes

When updating manifest from a non-checkout put changes into local_changes section