note: rename the id getter to git_note_id()

This was left over when we did the general switch.
index: rename an entry's id to 'id'

This was not converted when we converted the rest, so do it now.
commit: remvoe legacy 'oid' naming
tree: remove legacy 'oid' naming

Rename git_tree_entry_byoid() to _byid() as per the convention.
diff: rename the file's 'oid' to 'id'

In the same vein as the previous commits in this series.
diff: change id abbrev option's name to id_abbrev

Same as the other commits in the series, we use 'id' when talking about
thing rather than the datatype.
merge: rename _oid() -> id()

Following the rest of the series, use 'id' when refering to the value.
Merge pull request #2075 from libgit2/cmn/leftover-oid

Leftover OID -> ID changes