Is there anyway to "get credit" for post Masters work on a resume? I quit my PhD in physics about a year and a half ago. I started school in 2011, got my token Masters in 2013, and passed my quals. I then did about 2.5 years of research, mostly coding, to verify the theoretical models my advisor and I were working on.  

This actually turned me on to high performance computing. Combine this with a distaste for poverty and I jumped ship to be a software engineer.  Now I'm looking at a promotion and I'm trying to get credit for my time working as a developer for my advisor.  HR "requires" 3 years of professional experience for promotion to the level I'm trying to achieve.  

Can I spin the time as a sort of free lance dev? If so,  how? I refuse to let HR dismiss this developmental time of my career.
Research assistant is a job as well as part of an education, and it is common to see it listed as part of one's appointments on an academic CV.  After all, you are being paid for the work you do (even if typically at a subsistence level).

It would thus seem quite reasonable to list it that way on an industrial resume as well, as part of your list of prior employment, thereby providing a clear statement of your time working in that capacity.  Whether your HR department is reasonable enough to accept this or not is an entirely unrelated question, I'm afraid.