checker superfluously reports errors of library dependencies

[jurgenvinju]

Describe the bug

To reproduce:

1. clone java-air project
2. call mvn rascal:compile
3. read the errors. This lists a number of "deprecation" warnings (namely of deprecated functions calling other deprecated functions) in the ParseTree module.

After talking about it in slack with @DavyLandman and @PaulKlint it seems that the main check function that returns the list of modules (program(loc src, list[Message])) including program nodes for library modules. It seems that the program(...) nodes that come straight from PathConfig.libs tmodels and not via PathConfig.srcs files should be filtered or not end up in the list at all.

• behavior of VScode would align with this, since for every project the compiler is called, and if we keep the old behavior this would require deduplication or filtering.
• behavior of the mvn rascal:compile command would improve if we fix this issue. We don't want to report errors which are unfixable from the perspective of the current project (newbie users can not fix issues in the standard library for example).