Reland [mlir] Remove uses of LLVM's legacy pass manager

Use the new pass manager.

This also removes the ability to run arbitrary sets of passes. Not sure if this functionality is used, but it doesn't seem to be tested.

No need to initialize passes outside of constructing the PassBuilder with the new pass manager.

Reland: Fixed custom calls to `-lower-matrix-intrinsics` in integration tests by replacing them with `-O0 -enable-matrix`.

Reviewed By: mehdi_amini

Differential Revision: https://reviews.llvm.org/D123425