Discussion suggests that flowcharts are not useful or accurate.
The accuracy depends on how the flowcharts are constructed. If they are created manually, they are similar to any other document created manually and will become obsolete almost instantly; which makes manual flowcharts really worthless, so people tend to look at the code.
[The rest of this answer violates the OPs requirement "not interested in software (for creating flowcharts)" because I believe that the only way to get them in some useful form.]
If flowcharts are generated from code using a suitable tool for precise language analysis, they will be accurate. See Examples at http://www.semanticdesigns.com/Products/DMS/FlowAnalysis.html These examples are semantically accurate, although the pages do not have exact semantics, but this is only a part of the documentation.
It’s hard to find the following tools: -} especially if you need flowcharts that span multiple languages and several “execution paradigms” (the OP wants its INI files to be included, these are some kind of implied assignment statements, and I'm pretty sure that he will want to simulate SQL actions that are not flowcharts because they tend to be pure computation over tables).
It is also unclear that such flowcharts are useful. The examples on my page should be semi-conceptual; if you take into account all the microscopic details (for example, the possibility of an arc of the ABORT control flow coming from each call of the subroutine [since each call may cause an exception]), these diagrams become terribly large, fast. The fact that charts take up a lot of space (boxes, diamonds, lines, lots of spaces) makes this pretty bad. Once they become large, you literally get lost in space after arcs. Again, a good reason for people to avoid block diagrams for entire systems. (Another reason why people love text languages, in fact they can be quite dense, you can get a lot on the page with a short language and wait until you see APL :)
They can be of little help in individual functions if the function has complex logic.
I think it is unlikely that you are going to get accurate language analyzers that produce flowcharts for all languages that you want such anlayzers to correctly compose their flowcharts (you want JavaScript to call C #, which runs SQL ...?)
What you can hope for is a compromise solution: display the code with various hyperlinks to other artifacts that are referenced. You still need the ability to create such hyperlinks (see http://www.semanticdesigns.com/Products/Formatters/JavaBrowser.html for one way this might work), but you also need hyperlinks across the entire border language.
I do not know the tools that do this now. And I doubt that you have an interest or willpower to create such tools yourself.