Revision and cleanup of package dependencies

[almeidaxan]

As I remember while developing bfast-explorer, some packages were used just for one or two specific functions. I think it is important to check if these functions are really necessary, while also doing a clean-up of the code.

• Check for packages that are not used at all and remove them
• Ditch packages whose functions can be replaced by required packages' function and/or base functions
• Add the package's names to functions calls (i.e. <package_name>::). IMO this helps tracking which packages are being used and which are not