[FR] Add ability to run script on R files prior to sending to pandoc

[cjdbarlow]

Problem:

• The current before\after_chapter_script features don't allow changes to file contents
• I would like to add a script that can edit content (but leave the underlying file unchanged)
• I would like to do this prior to merging, so that changes can be targeted and configured at the file level
• An example is custom shortcodes which can have dynamic elements (adjusted on a per file basis, e.g. via YAML header)
• This means writing can remain clean and non-technical, whilst allowing more complex page elements to be created

Ideal solution:

• Specify a script or list of scripts in the _bookdown.yml that modify file contents prior to merging

Current solution:

• My current solution alters the merge_chapters function and runs an R script to alter the character vector (x) containing the lines of each file
• Files can be identified (by f) so scripts can identify any relevant YAML in that file and alter their action appropriately
• There's probably a cleaner way to do this