[llvm-objcopy] Fix bug in how segment alignment was being handled

Just aligning segment offsets to segment alignment is incorrect and also
wastes more space than is needed. The requirement is that p_offset ==
p_addr modulo p_align *not* that p_offset == 0 modulo p_align. Generally
speaking we've been using p_addr == 0 modulo p_align. In fact yaml2obj
can't even produce a valid situation which causes llvm-objcopy to
produce incorrect results because alignment and offset were both
inherited from the sections the program header covers. This change fixes
this bad behavior in llvm-objcopy.

Differential Revision: https://reviews.llvm.org/D39132

llvm-svn: 317284