Resolve "Make DataManager and PlotManager output directories more configurable"

What does this MR do?

This MR makes the behaviour of DataManager and PlotManager regarding their out_dir more configurable by exposing some parameters.

Other minor tweaks and changes

• It introduces a minor breaking change by renaming the format string segment date to timestamp.
• tools module yaml functions now accept write and read modes and write --- yaml prefix
• PlotManager now takes cfg_exists_action to handle a potentially already existing plot configuration file.

Can this MR be accepted?

• Implemented the changes
• Tests added or adjusted
• Pipeline passes
• Changelog entry added
• Bumped version to 0.6.0-pre.0

Anything to double-check?

Nope.

Related issues

Closes #36 (closed)

Some features required in utopia/utopia!183