refactoring .in files

[frenkiboy]

Develop a system without the .in files - i.e. have a local config/settings file which would define which filea need to be changed during the configuration steps (which would also enable much easier documentation of such files). The reason for this is that the .in suffix makes the development much harder, specially when it appears on scripts.

[rekado]

This is essentially about removing @VERSION@ from the Rmd files. This value could instead be passed as an argument by the pipeline driver script.

[rekado]

The problem with replacing configure templates is that we aim to do all work at configure time and not at runtime. Yes, having fewer files that need substitutions would be great, but to remove configure time substitutiton and replace it with a runtime lookup means that we must have a globally accessible file that can be included at runtime by all files needing substitutions.

The configure.ac file does in fact list all files that have placeholders (see AC_CONFIG_FILES).

As it is this issue is a little too broad, so I don't think it's actionable. Is there a specific issue with specific files? Perhaps this issue could be repurposed to focus on one such issue and find a solution for it. Otherwise I'd like to close it.