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Refactoring includes in (fd, ucc, pipelines)

All files that do not fit into the category above were either obtained using clang-format-18, or were slightly modified to build project correctly.

About include comments: it's temporary and they don't make sense.

This PR is one of the 3 parts of the larger #531. And it's also Draft, because I need to clean up the comments and run IWYU for full improvement.

- "test_typo_miner.cpp" requires GetAllDerived from "algorithms/create_algorithm.h"
- refactoring includes in (fd, ucc, pipelines)
These files are not part of the main idea of this PR
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