rugnux: move rugnux_cli.cpp from tools/ to rugnux/

The offline analysis CLI belongs next to its Rugnux library. Move the source and
the ADD_EXECUTABLE(rugnux ...) target (plus the Windows wingetopt link) into
rugnux/CMakeLists.txt; the ../reader, ../common, ../image_analysis includes are
unchanged (both dirs sit one level under the root) and ../rugnux/Rugnux.h becomes
a local Rugnux.h. rugnux/ is added before tools/ in every build config, so
viewer-only and Windows packages still get the CLI.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

rugnux/CMakeLists.txt

@@ -9,3 +9,14 @@ ADD_LIBRARY(Rugnux STATIC
 )
 
 TARGET_LINK_LIBRARIES(Rugnux JFJochReader JFJochImageAnalysis JFJochWriter)
+
+# rugnux is the single offline analysis CLI: full pipeline by default, plus --azint-only
+# (azimuthal integration) and --scale (re-scale/merge stored reflections) modes.
+ADD_EXECUTABLE(rugnux rugnux_cli.cpp)
+TARGET_LINK_LIBRARIES(rugnux Rugnux JFJochReader JFJochImageAnalysis JFJochWriter)
+INSTALL(TARGETS rugnux RUNTIME COMPONENT viewer)
+
+# On Windows this CLI gets getopt/getopt_long from the vendored wingetopt shim (libc has none).
+IF (WIN32)
+    TARGET_LINK_LIBRARIES(rugnux wingetopt)
+ENDIF()

rugnux/rugnux_cli.cpp

@@ -28,7 +28,7 @@
 #include "../image_analysis/scale_merge/ResolutionCutoff.h"
 #include "../image_analysis/scale_merge/TwinningAnalysis.h"
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"
-#include "../rugnux/Rugnux.h"
+#include "Rugnux.h"
 
 // Default rot3d per-frame scale-G smoothing range (XDS DELPHI-like), in degrees of rotation.
 constexpr double SMOOTH_G_DEFAULT_DEG = 5.0;

tools/CMakeLists.txt

@@ -8,11 +8,7 @@ ADD_EXECUTABLE(jfjoch_extract_hkl jfjoch_extract_hkl.cpp
 TARGET_LINK_LIBRARIES(jfjoch_extract_hkl JFJochReader)
 INSTALL(TARGETS jfjoch_extract_hkl RUNTIME COMPONENT viewer)
 
-# rugnux is the single offline analysis CLI: full pipeline by default, plus --azint-only
+# rugnux, the single offline analysis CLI, lives in rugnux/ next to its library.
-# (azimuthal integration) and --scale (re-scale/merge stored reflections) modes.
-ADD_EXECUTABLE(rugnux rugnux_cli.cpp)
-TARGET_LINK_LIBRARIES(rugnux Rugnux JFJochReader JFJochImageAnalysis JFJochWriter)
-INSTALL(TARGETS rugnux RUNTIME COMPONENT viewer)
 
 # In-place re-compress /entry/data/data of a _data file from bitshuffle/LZ4 to bitshuffle/zstd.
 ADD_EXECUTABLE(jfjoch_recompress jfjoch_recompress.cpp)
@@ -22,7 +18,6 @@ INSTALL(TARGETS jfjoch_recompress RUNTIME COMPONENT viewer)
 # On Windows these CLIs get getopt/getopt_long from the vendored wingetopt shim (libc has none).
 IF (WIN32)
     TARGET_LINK_LIBRARIES(jfjoch_extract_hkl wingetopt)
-    TARGET_LINK_LIBRARIES(rugnux wingetopt)
 ENDIF()
 
 # Online / hardware tools (broker, FPGA, receiver, detector). They link the non-portable