fix(arm): keep CMakeFiles/ between make TOPP and make pyopenms

After the two-pass cmake configure landed in 5185c3e, the next
attempt got past `make -j4 TOPP` (the link error is fixed) but
failed fast in `make -j4 pyopenms` with:

    CMake Error: Not a file: /openms-build/CMakeFiles/VerifyGlobs.cmake
    CMake Error: Error processing file: /openms-build/CMakeFiles/VerifyGlobs.cmake
    make: *** [Makefile:11553: cmake_check_build_system] Error 1

`VerifyGlobs.cmake` is generated by cmake for `file(GLOB CONFIGURE_DEPENDS ...)`
targets and is consulted by `cmake_check_build_system` at the top of
every subsequent `make` invocation. The intermediate cleanup line

    RUN rm -rf src doc CMakeFiles

deleted it, which is fine on the x86 single-pass build (different
cmake codepath when PYOPENMS=ON is set in the initial configure, no
VerifyGlobs.cmake generated) but breaks the ARM two-pass build.

Stop deleting CMakeFiles/ between `make TOPP` and `make pyopenms`.
We still drop `src/` and `doc/` for disk savings; keeping CMakeFiles
costs only a few hundred MB on the intermediate layer.

Author: claude

Dockerfile.arm

@@ -108,7 +108,16 @@ RUN cmake -DPYOPENMS=ON -DPY_MEMLEAK_DISABLE=On -DCMAKE_IGNORE_PREFIX_PATH=/root
 
 # Build TOPP tools and clean up.
 RUN make -j4 TOPP
-RUN rm -rf src doc CMakeFiles
+# NOTE: do NOT delete CMakeFiles/ here. The two-pass cmake configure used
+# above generates CMakeFiles/VerifyGlobs.cmake for the pyOpenMS targets'
+# CONFIGURE_DEPENDS globs; the next `make -j4 pyopenms` runs
+# `cmake_check_build_system` which fails fast if VerifyGlobs.cmake is gone:
+#   CMake Error: Not a file: /openms-build/CMakeFiles/VerifyGlobs.cmake
+# The x86 single-pass build seems to avoid generating that file (different
+# cmake codepath when PYOPENMS is set during the initial configure), which
+# is why it can still `rm -rf CMakeFiles` here. CMakeFiles/ adds ~a few
+# hundred MB to the intermediate layer — acceptable.
+RUN rm -rf src doc
 
 # Build pyOpenMS wheels and install via pip.
 RUN make -j4 pyopenms