Thank god for version control and being able to rescue yourself from stupidity. Obviously the rm * was not what I was going for; I had wanted to just kill the patch files.

dmcgee@galway /home/dmcgee/projects/pacman (patchreview)
$ ls
0001-Introduce-D-database.patch                                  INSTALL               autoclean.sh    debugconfig.sh       po
0002-Change-Y-n-to-y-N-with-REMOVE_PKGS-remove_unresolvab.patch  Makefile              autogen.sh      depcomp              proto.install
0003-Re-add-the-non-user-friendly-ask-option.patch               Makefile.am           autom4te.cache  dload-thoughts.txt   runpactest-lt.sh
0004-Do-not-remove-conflict-by-default.patch                     Makefile.in           config.guess    doc                  runpactest.sh
0005-Re-enable-REMOVE_PKGS-test-in-pactest-suite.patch           NEWS                  config.h        etc                  scripts
0006-Add-a-new-reason-field-to-pmconflict_t-struct.patch         PKGBUILD-split.proto  config.h.in     install-sh           src
0007-Use-sync.c-for-upgrade-transaction-prepare-and-commi.patch  PKGBUILD.proto        config.log      lib                  stamp-h1
0008-Remove-trans-type.patch                                     README                config.rpath    libtool              tags
0009-Change-the-interface-for-target-loading.patch               TODO.aaron            config.status   ltmain.sh            valgrind.supp
AUTHORS                                                          TODO.dan              config.sub      missing
COPYING                                                          TRANSLATORS           configure       mkinstalldirs
ChangeLog.proto                                                  acinclude.m4          configure.ac    pacman-3.3.0.tar.gz
HACKING                                                          aclocal.m4            contrib         pactest

dmcgee@galway /home/dmcgee/projects/pacman (patchreview)
$ rm *
rm: cannot remove `autom4te.cache': Is a directory
rm: cannot remove `contrib': Is a directory
rm: cannot remove `doc': Is a directory
rm: cannot remove `etc': Is a directory
rm: cannot remove `lib': Is a directory
rm: cannot remove `pactest': Is a directory
rm: cannot remove `po': Is a directory
rm: cannot remove `scripts': Is a directory
rm: cannot remove `src': Is a directory

dmcgee@galway /home/dmcgee/projects/pacman (patchreview)
$ ls
autom4te.cache  contrib  doc  etc  lib  pactest  po  scripts  src

A simple git checkout -- . and I was mostly back in business, outside of the autogen stuff and my custom little helper scripts that I hope I can dig up elsewhere and one text file that was just some broken psuedocode anyway.