Fix bug:

- Assume X and Y depend on Z
- X and Y both compile clean.
- A change is made to Z
- X and Y are now "out-of-date," and marked to compile.
- The change causes a failure in X, but Y still compiles clean.
- Because X compiles clean, the database will be updated and store the new mtime of Z!
- Attempting to compile again, the mtime of Z will not be considered "changed" since the last compile.
- X depends on Z, but Z is not marked "changed," and X will not be recompiled, even though it is still in a dirty state!
- Linking of X and Y produces wild results. UB. ORD NDR. Badness.

The fix is to have the edges in the graph between inputs and outputs
store the mtime of the input, rather than to store that mtime on the
file itself. Thus, each individual relationship between inputs and
outputs will track the "outdated-ness" of themselves.

This also adds a test which can correctly reproduce the issue in absense of the fix.