[remaining complex shuffling action that mimics what's needed in SVN, snipped]
Git is not SVN; do not expect it to behave *like* SVN.
In particular, Git does not have file history. Git has only commits.
SVN has commits, but SVN commits contain file history. In Git, the commits *are* the history, and are the *only history*. Each commit has a full snapshot of every file, under the names you told Git to use, with the contents that you told Git to save.
The command `git log science/dynare` tells Git: Look through commits, one by one, and whenever there's a file whose name starts with `science/dynare` that's different in *this* commit, vs the previous one, tell me about this commit. Since the old commits have files named `math/dynare/something` instead, Git doesn't tell you about them.
The `git log` command has a flag, `--follow`, that has a trick up its sleeve (wait: does `git log` have sleeves? well, anyway). This trick is a bit limited though. Let's say there's a README file in the science/dynare/ directory, as of the latest commit. If you run:
git log --follow science/dynare/README
Git will look at *this* commit and find the file, and will look at this commit's *parent* and *not* find the file, because the parent does not have `science/dynare/README` in it. But the parent does have `math/dynare/README` in it *and that file exactly matches* this commit's copy. So `git log` will tell you about this commit and say that the file was *renamed*. From this point backwards, `git log` will be looking, not for `science/dynare/README`, but instead for `math/dynare/README`.
Unfortunately, the `--follow` trick only works on *one file*. But it will let you know that if you re-run your `git log` with `math/dynare` you can see what happened before the renaming.
A future `git log` really should be smarter about detecting the whole-subtree renaming, and be able to follow it. This won't require any change in the repository, just a smarter `git log`. But someone has to write that smarter `git log`.
Chris
