More file path improvements, mostly around pipeline jobs (#1203)

Author: labkey-jeckels

server/bootstrap/src/org/labkey/bootstrap/LabKeyBootstrapClassLoader.java

@@ -210,7 +210,7 @@ public void validateReplaceArchive(File explodedModuleDirectory, File updatedArc
  @Override
  public Map.Entry<File,File> updateModule(File explodedModuleDirectory, File updateArchive, File existingArchive, File mvExistingArchive, boolean dryRun) throws IOException
  {
- File updateArchiveNewHome = new File(existingArchive.getParent(), updateArchive.getName());
+ File updateArchiveNewHome = new File(existingArchive.getParentFile(), updateArchive.getName());
 
  validateReplaceArchive(explodedModuleDirectory, updateArchive, existingArchive);