Logger overhaul

[RasmusSkytte]

Intent

This PR introduces an overhaul for the Logger to make it simpler to use in different cases.

Approach

• The Logger was re-factored

• The LoggerNull class was added, which matches the structure of Logger but does not write logs to console, file or DB.

• Fields that were previously public are now made private with corresponding active bindings to show their values.

• The db_tablestring argument was replaced with db_table and made more flexible:
  i.e. it now takes id-like objects instead of only a character string.

• The ts argument was renamed to timestamp to match update_snapshot()

• $log_info(), $log_warn() and $log_error() were adjusted.

  • The message produced by $log_info() is now return invisibly to simplify $log_warn() and $log_error().
  • The message in $log_info() is printed with message() instead of cat() to allow the suppression of output (CRAN best practices).

• A custom logging format for timestamps can be passed to the $log_*() functions via the argument timestamp_format or the option "SCDB.log_timestamp_format" (fixes FEATURE: Custom logger format #65).

• The tests for Logger were made specific (ie. the single large test was broken into several tests).
  In addition extra checks are made during testing to ensure "info", "warnings" and "errors" work as intended for different combinations of logging to file and logging to console.

• checkmate assertions improved when log_conn = NULL

• return statements gets their own line in accordance with coding standard.

Known issues

This PR also contains the code being merged in

• Move functions to separate files #95
• Delete intermediate tables after use #89

Once merged, this PR will be rebased and opened.

Checklist

• The PR passes all local unit tests
• I have documented any new features introduced
• If the PR adds a new feature, please add an entry in NEWS.md
• A reviewer is assigned to this PR

[LasseEngboChr]

Only a few suggestions

[LasseEngboChr]

One line in documentation should be deleted.