Fix source deps bug in dependency analysis.

- Not all dependencies were getting computed correctly, because the source_deps section
 of the analysis relations file wasn't getting used. (It was removed because it appeared
 to be redundant, and caused some trouble with error message generation.) This reinstates
 source_deps in the analysis.

Auditors: benjy
Dependency analysis fixes.

- Add a filter parameter for eliminating missing dependency errors that
  shouldn't be reported.
- Only return missing dependency errors if they were reported to the user.
- Throw exception when missing deps are detected.
- Eliminate redundant retrievals of parameters.

Auditors:  benjy
Address review comments.
Merge branch 'source-deps-fix'