Use MySQL credentials in ~/.my.cnf instead of inst/config/database.R

[paulrougieux]

Storing MySQL credentials in ~/.my.cnf might be problematic for web server processes.

There is a Stackoverflow Q&A about how to set MySQL connection parameters for Shiny.

2 options to tell R where the MySQL credential are located :
(1) Add a default.file argument to each function that generate reports and uses RMySQL::dbconnet() in the background.
(2) create a function that set an option locating "my.cnf" for the duration of the R session.

[paulrougieux]

Started deprecating function that use the old way to connect to the database in commit e50ddf9.