Repo add file enhancement

[thereseanders]

This PR conducts a number of changes on repo_add_file()`

• Adds folder parameter to the repo_add_file() function. It is NULL by default. This change is necessary to allow the usage of repo_add_file() with the new peer review functions, for example to batch place reviewer feedback forms into author-specific folders on a reviewers' repositories.
• Updates/changes the documentation and examples.
• Removes unnecessary parameters from purrr::walk
• Removes turning empty message into list (causes repo_put_file to fail).

[thereseanders]

Changed the check_file_modification test to file_exists. The current form of check_file_modification will return TRUE on deleted files and won't allow to add new files. This causes functions calling repo_add_file to fail.

We should talk about whether we want to include the check_file_modification again that checks for student versus admin modifications.

[thereseanders]

Based on our conversation, I implemented the following:

1. Changed file_exists() to file_exists_current()
2. Wrote new function file_exists() that uses check_file_modification() to see whether file ever exists, and only if TRUE is returned uses file_exists_current() (that is costly in terms of calls to the API).

Currently not implemented

• Check and message who modified file.
• Potentially use GET call to check for existence of file rather than check_file_modification ()

[thereseanders]

I made more modifications on repo_add_file() and helper functions.

1. Changed file_exists() to file_exists_current()
2. repo_add_file() now calls check_file_modification() as part of the commit messaging.
3. added new function check_file_everexist() that checks for a length of the output of get_committer() > 0.
4. Only if check_file_everexist() evaluates to true is the costly call to file_exists_current() implemented. We should think about whether to replace this functionality with a GET call instead.
5. I will use a purrr::safely(github_api_repo_get_file)() call in the peer review functions whenever possible to reduce calls to check_file_everexist().

[thereseanders]

In the new version, PR makes the following changes:

• adds folder parameter to repo_add_file()
• enhances error message for file_status by printing specifically which file could not be found
• changes file_exist() to use new repo_files() function (that relies on github_api_repo_get_tree()).
• repo_add_file() calls file_exist(), rather than check_file_modification() when deciding whether to add file.
• check_file_modification() is called in the messaging if the file exists and overwrite == F
• merged upstream changes
• Updates/changes the documentation and examples.
• Removes unnecessary parameters from purrr::walk
• Removes turning empty message into list (causes repo_put_file to fail).

[rundel]

Looks good, I made a slight simplifying change to use fs instead of a regex to prepend the folder to the repo path.

[rundel]

Only small concern I have is that I found the folder parameter name slightly confusing without reading the docs. Since this refers to something that will happen only in the repository maybe consider a prefix like repo_ or dest_ (neither are particularly satisfying but I dont have a better suggestion atm).

[thereseanders]

Oh the fs::path() solution is great. Thank you!

I changed the folder parameter to repo_folder.