[Issue#147]: # This is a combination of 49 commits.

[Issue#147]: Added flag to mark variables used in external calls

[Issue#147]: Function to fill vault has been excorporated. Now makeVault assigns ids to all real variables: these were lines that got lost in refactoring.

[Issue#147]: Modified main of Modify code. Now 1) read the banned_var list + vault 2) add var used in external calls to ban list 3) propagate dependency of the ban list

[Issue#147]: Moved function change_code form inserter to ModifyCode

[Issue#147]: Moved function from Inseter + var used in external have to be banned just if they are RPE type

[Issue#147]: Added additional parameter "var_type" for tracking function

[Issue#147]: Added incremental_id to variables, to be used during tracking.

[Issue#147]: Added var_type to function that propagate dependency. Now var_identifier uses var.incremental_number

[Issue#147]: Added tracking of RPE variables

[Issue#147]: Modified function load_sources to take extension as input, and to be able to read files in subdirectories

[Issue#147]: Extension is now passed to create ReadSourceFile objects, to properly set module_name

[Issue#147]: Updated rebuild_text, so as to split lines with \n marker in module.lines

[Issue#147]: Moved all function to deal with non preprocessed code into a single file

[Issue#147]: Added parameter to read file to avoid removing spaces when reading. Fixed bug in write_file that was adding a last empty line to every file.

[Issue#147]: Check that, when looking for allocation of a var  we did not match a member with the same name: a_i will also match %a_i

[Issue#147]: Storing precision with and without KIND keyword specification was useless: removed