Change variables and enhance documentation

[Andreas-Piter]

Enhance the documentation and make the software and its parameters more intuitive for other users.

• Change names in configuration file.
• Combine three config sections to a general section.
• Remove obsolete check w.r.t. second-order points in densification step.
• Create smaller logo.
• Use json5 to allow comments in the config.json.
• Check if required intermediate results are available before running a step.
• Change name of DEM error to DEM correction in any log messages to avoid confusions with real errors.