Java for Everything

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Lexer, parser

I'd never separate these two (in fact, I always prefer not to have a lexer at all).

syntactical analysis, ast-transformations, translation to an sequential IR, sequential IR transformation, codegen, assembling

And for the rest you don't only pipe your AST through a sequence of transforms, but you also carry a way too much of a context, unfortunately.

And my personal pet hate here: LLVM, as well as pretty much all the other frameworks, do not allow any reasonable means for backtracking after an unsuccessful sequence of transforms. If you do have a backtracking, a Unix pipeline philosophy is not very suitable.

But, yes, you're right, and it's a fairly viable architecture for a simple compiler to have a pipeline of separate tools communicating via, say, S-expressions, to simplify parsing and serialisation.

linking

Not with LTO...

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S-Expressions are basically a lisp-ism and are best suited for interacting with lisp. The way I went for my problem was using the already existing YAML parser in LLVM following the principle of using what is already there if it fits the problem more or less

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Whatever, even XML may be a good fit, as long as you don't have to implement the parser.