CMake/Ninja attempting to compile deleted `.cpp` f

I've found that when I delete cpp files from my project using cmake and ninja, I can't easily compile it without first completely deleting my build directory and starting from scratch. CMake and/or Ninja apparently squirrels away a number of references to all the cpp files that it compiles, even deleting the CMake cache before re-running CMake doesn't remove all the references.

Is this a known issue? Is there a solution? I've occasionally just run rm $(grep -R <filename> <builddir>), but that's a terrible kludge.

EDIT: It appears I was mistaken, as I have not been able to duplicate this problem. Manually re-running CMake appears to always generate the correct list of .cpp files, even using GLOB to generate lists of sources.

Turning my comments into an answer

Collecting your source files with `file(GLOB ...)`

Yes, CMake won't know about new or deleted source files when collecting your source files with the file(GLOB ...) command. This is a known restriction with CMake. I've changed my CMake project(s) to list all source files individually exactly because of this. Out of convenience I'm still collecting my header files with the file(GLOB ...) command.

Quoting from CMake's file() command documentation:

We do not recommend using GLOB to collect a list of source files from your source tree. If no CMakeLists.txt file changes when a source is added or removed then the generated build system cannot know when to ask CMake to regenerate.

Deleting `CMakeCache.txt` to retrigger Configuration

Just deleting CMakeCache.txt may not be enough to retrigger the CMake configuration. Issue 0014820: warn users about removing only CMakeCache.txt claims you need also to delete all CMakeFiles directories.

From my experience the most reliable way to retrigger the CMake configuration is to touch one of the projects CMakeLists.txt files.

Note: For ninja CMake adds a rebuild_cache target for conveniently running CMake for your project again.

Retrigger after Updates from Source Control

Just one thought: if the deletion of source files happens because they were removed from your source control there maybe a workaround that still allows you to use file(GLOB ...) on your source files.

E.g. if you use GIT you could add the following to your main CMakeLists.txt:

configure_file(${CMAKE_SOURCE_DIR}/.git/index ${PROJECT_BINARY_DIR}/git_index.tmp)

Disadvantage: It would retrigger configuration which each GIT operation (update, commit, ...).

Some References:

run cmake when adding file in eclipse
CMake: Correct way to make an arbitrary file trigger