Fix \include of files in subdirectories

Since we direct TeX to write output files to a separate output
directory, any files \included from a subdirectory will cause TeX to
attempt to create an output file in a parallel subdirectory of the
output directory, which is likely not to exist.

Technically this is a TeX problem (anyone using -output-directory with
\include of files from subdirectories would encounter this), but since
latexrun opts the user in to -output-directory, it seems best for
latexrun to mask this problem by creating this parallel output tree.
Fix BibTeX error parsing case

Given an error like

I couldn't open auxiliary file biblio.aux
---line 3 of file latex.out/main.aux

the regexp this previously used would consume the first '-' as an
error message and thus ignore the previous line.  Add lazyness to the
regexp so that the message on the second line is the empty string and
we fall back to the previous line.