MOD-1000: Improve documentation, add docstrings, update versions

remove MOD-1007: Enhance Code Quality Automation (Medium)

Move tasks from AGENTS to TODO stories

MOD-1002: Code formatting and style enforcement completed

number stories using format MOD-XXXX, where XXXX starts with 1000

wip: fix tests

Replace print() with logging module, add --log-level CLI argument

actualize line numbers

add AGENTS.md, TODO.md

WIP: test circular deps

add missing expected files list in test_dir_circular_dependencies_impl

add test_dir_circular_dependencies_impl_cmake testcase

add testcase test_dir_simple_cmake which runs cmake with clang-20, clang-21, gcc-15

circular dependencies in implementation units without partitions

add assert on cycle

find circular dependencies between modules

refactoring: extract `FileProcessingState`

refactoring: _add builder methods

refactoring joint builder for nicer architecture

joint modules: allow having header named the same way as joint module