Switch every project-local #include "..." to use the path relative to the
repository root, e.g.

  #include "src/forcefields/mmff.h"
  #include "rdkit_extensions/mmff_flattened_builder.h"
  #include "tests/test_utils.h"

Bare neighbor includes ("foo.h"), upward-relative includes ("../foo.h"), and
angle-bracket project-local includes (<foo.h>) are no longer accepted.

Mechanism:
- Add an INTERFACE library nvmolkit_include_root (in the root CMakeLists.txt)
  that exports ${PROJECT_SOURCE_DIR} as its include path. A single
  link_libraries(nvmolkit_include_root) just before the project subdirectories
  applies it to every first-party target.
- Drop the previous per-target target_include_directories(...
  ${CMAKE_CURRENT_SOURCE_DIR}) and ${PROJECT_SOURCE_DIR}/... entries that
  existed only to expose project headers via library include dirs. They are
  now redundant.
- Drop a couple of dead include paths (nvmolkit/utils does not exist;
  smarts_filter no longer needs ${PROJECT_SOURCE_DIR}/src once the include
  rewrite happens).

Add admin/run_include_check.sh + admin/include_check.py to enforce the
policy. Default mode rewrites in place, -d / --check mode reports violations
and exits non-zero. Wired into .github/workflows/lint.yml as a new
include-check job alongside clang-format, cmake-format, and ruff-format.

Configure, build, and ctest pass.