Update JIRA references in TODO, remove finished items

JIRA's structure has been reorganized, so change the JIRA issue
references to be accurate again.  Add JIRA issues for the things
that hadn't been entered into JIRA yet.

Change-Id: I385d19b09108d94430bbe142a2b3f6f80b5e4c39
Reviewed-on: https://gerrit.stanford.edu/1588
Reviewed-by: Russ Allbery <rra@stanford.edu>
Tested-by: Russ Allbery <rra@stanford.edu>