I attempted to fix this in commit c06d1fba40, but it was apparently
incomplete and not all cases were covered by tests.
Let's add a much more thorough test by going through every possible
combination and making sure redo-{sources,targets,ood} all work as
expected, that the "you modified it" warning does or does not show up
when expected, and that dependencies are rebuilt the number of times we
expect.
When we check dependencies and a previously-is_generated dependency
existed before, but no longer does, forget that it was is_generated.
This slightly improves the situation where as a project evolves, a file
that used to be a target gets removed, and then later is re-added as a
static source file. (It doesn't fix the other variant, where a file is
changed from target to source in a single atomic change, and is never
missing. That one will be trickier to handle.)
While adding a test for this behaviour, I discovered that redo-sources,
redo-targets, and redo-ood were reporting their output relative to
STARTDIR instead of relative to $PWD, so fix that too.
