Enable argument 'all' to commit multiple modified (or deleted) files.

[jdblischak]

I observed the behavior that setting the argument all = TRUE for commit only commits one tracked file instead of all tracked files. The unit tests only test for one modified file or one deleted file. I think the issue is from line #155 in commit.r. s$unstaged is a named list, thus passing s$unstaged$modified to lapply is only passing one element of the list. Here's a small example to illustrate:

s <- list(unstaged = list(modified = "file1.txt", modified = "file2.txt"))
lapply(s$unstaged$modified, function(x) x)
## [[1]]
## [1] "file1.txt"

I updated commit so that it will iterate over all tracked files and also added some unit tests. I was able to run make check successfully with R 3.4.0 on Ubuntu 16.10. Please let me know if you would like me to make any modifications.

[coveralls]

Coverage increased (+0.008%) to 78.026% when pulling bcc1056 on jdblischak:commit-all into 1a1c392 on ropensci:master.

[stewid]

Thanks for finding the bug and fixing it, much appreciated.

Cheers
Stefan