Refactoring .hpp -> .h, .cpp and remove class templates

[mrp089]

This is equivalent to #41 but leaves the file history intact. Closes #36.

Do not squash and merge to leave history intact.

[mrp089]

Steps to create new files while preserving the history:

1. Create .cpp files from .hpp

git mv FILE.hpp FILE.cpp
git commit

2. Reset .hpp files

SAVED=`git rev-parse HEAD`
git reset --hard HEAD^

3. Create .h files from .hpp

git mv FILE.hpp FILE.h
git commit

4. Merge commits to have both .cpp and .h files

git merge $SAVED
git commit -a

[mrp089]

I manually recreated the file structure in @ktbolt's branch using git mv.

Since we can't do a squash and merge in this pull request, I already squashed @ktbolt's 21 commits into one using an interactive rebase (marking all but the first commit as squash):

git rebase -i HEAD~25

Finally, I applied @ktbolt's changes by creating a diff to the rebased branch with git diff and applied it as a patch with git apply to only change file contents but not the files themselves. I then commited that with @ktbolt as an author - the perfect crime!

[mrp089]

Note that there are still many files shown as newly created. However, this is just a GitHub problem (I assume it can't show two files as moved from the same original one).

If you do a git blame on one of the "newly created" files (e.g. BloodVessel), you get the full history.

[mrp089]

@ktbolt, @menon-karthik I'll fix the Doxygen documentation. It doesn't find the files anymore and many comments need to be updated.

[mrp089]

Done! There are a few more Doxygen warnings, see #46, but nothing that should prevent this from being merged.

[menon-karthik]

Mostly looks good to me! I just have a few comments.

Thanks @ktbolt and @mrp089 for doing this!

[menon-karthik]

@ktbolt Just wondering why this wasn't required previously?

[ktbolt]

@menon-karthik The current version creates object files that are linked into the interface shared libraries so they need to have relative addresses.

[menon-karthik]

@ktbolt Do we really need to call this zd_model instead of just model?

[ktbolt]

@menon-karthik Oops, meant to rename that, was testing for name collision problems. I plan on removing namespaces in a later Issue.

[menon-karthik]

Git thinks many of these files are copied from src/io/namespace

[menon-karthik]

Just pointing this out, not saying it's something we should dig into.

[mrp089]

Yeah, that's weird. But I think it's just GitHub's diff display. In the history, it shows up correctly.

[ktbolt]

@mrp089 Thank you for getting all of this to work, my partner in crime!

[ktbolt]

Looks good!

Thanks a bunch @mrp089 and @menon-karthik for pushing this messy PR through.