Proteo wizard master

.gitattributes

@@ -4,4 +4,5 @@
 *.mzml binary
 *.mzxml binary
 
-*.sh text eol=lf
+*.sh text eol=lf
+*.jam text eol=lf

.gitignore

@@ -174,9 +174,6 @@ _TeamCity*
 *.coverage
 *.coveragexml
 
-# Visual Studio test playlists
-*.playlist
-
 # NCrunch
 _NCrunch_*
 .*crunch*.local.xml
@@ -229,11 +226,6 @@ PublishScripts/
 # NuGet v3's project.json files produces more ignorable files
 *.nuget.props
 *.nuget.targets
-# Spurious NuGet.Config regenerated in a .nuget folder nested inside another
-# .nuget folder (seen only on some machines, e.g. idpicker/.nuget/.nuget/); never
-# part of the project. Anchored to the nested case so the tracked top-level
-# idpicker/.nuget/ files (NuGet.Config, NuGet.exe, NuGet.targets) are unaffected.
-**/.nuget/.nuget/
 
 # Microsoft Azure Build Output
 csx/
@@ -387,14 +379,11 @@ build-nt-x86
 /libraries/msparser_*_win64
 /libraries/msparser_*_linux64
 /libraries/zlib*
-/libraries/zstd*
 Version.cpp
 /pwiz_tools/BiblioSpec/tests/inputs
 /pwiz_tools/BiblioSpec/tests/output
 /pwiz_tools/SeeMS/**/AssemblyInfo.cs
 /pwiz_tools/MSConvertGUI/**/AssemblyInfo.cs
-/pwiz_tools/Osprey/**/AssemblyInfo.cs
-/pwiz_tools/Osprey/dist/
 /pwiz_tools/Bumbershoot/**/*Version.cpp
 /pwiz_tools/Bumbershoot/**/AssemblyInfo.cpp
 /pwiz_tools/Bumbershoot/**/AssemblyInfo.cs
@@ -442,7 +431,6 @@ SkylineTester Results
 /b.bat
 /b64.bat
 /b32.bat
-/bo*.bat
 /bs.bat
 /bs64.bat
 /bs32.bat
@@ -465,9 +453,6 @@ SkylineTester Results
 /pwiz_tools/Skyline/SkylineTester/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/TestRunner/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/Executables/SkylineBatch/SkylineBatch/Properties/AssemblyInfo.cs
-/pwiz_tools/Skyline/Executables/AutoQC/AutoQC/Properties/AssemblyInfo.cs
-/pwiz_tools/Skyline/Executables/Tools/SkylineMcp/SkylineAiConnector/Properties/AssemblyInfo.cs
-/pwiz_tools/Skyline/Executables/Tools/SkylineMcp/SkylineMcpServer/Properties/AssemblyInfo.cs
 /pwiz_tools/Skyline/Executables/Installer/FileList64.txt
 /pwiz_tools/Skyline/TestSettings_x??.testsettings
 /pwiz_tools/Skyline/SignAfterPublishPW.bat
@@ -497,7 +482,16 @@ SkylineTester Results
 /tutorialTestNames.txt
 /tests.txt
 /pwiz_tools/Skyline/Translation/Scratch
+pwiz/data/vendor_readers/Agilent/Reader_Agilent_Test.data/ImsSynthCCS.mz
+pwiz/BrowseOnly/
+coutd.txt
+cout.txt
+cerrd.txt
+cerr.txt
+
+mt_tools/copy_lib.cmd
+mt_tools/pwiz-config-version.cmake
+mt_tools/pwiz-config.cmake
+
+/libraries/zstd-1.5.7/
 
-# AI tooling junction (created by build with --ai flag)
-/.claude
-ai/

mt_build.bat

@@ -0,0 +1,3 @@
+rem run from VC command prompt
+quickbuild.bat address-model=64 --i-agree-to-the-vendor-licenses --without-shimadzu --abbreviate-paths pwiz msconvert
+

mt_build_cvgen.bat

@@ -0,0 +1,3 @@
+quickbuild.bat address-model=64 --i-agree-to-the-vendor-licenses --without-bruker --without-sciex --without-shimadzu --without-waters  -j8 --abbreviate-paths pwiz/data/common//cvgen
+
+

mt_build_debug.bat

@@ -0,0 +1,3 @@
+rem run from VC command prompt
+quickbuild.bat address-model=64 variant=debug --i-agree-to-the-vendor-licenses --without-shimadzu --abbreviate-paths pwiz msconvert
+

mt_generate_cv.bat

@@ -0,0 +1,7 @@
+SET CVGEN_PATH=".\build-nt-x86\pwiz\data\common\msvc-14.3\rls\adrs-mdl-64\async-excpt-on\lnk-sttc\thrd-mlt"
+SET OBO_PATH=".\pwiz\data\common"
+
+%CVGEN_PATH%\cvgen.exe %OBO_PATH%\psi-ms.obo %OBO_PATH%\unimod.obo %OBO_PATH%\unit.obo %OBO_PATH%\imagingMS.obo
+
+copy %CVGEN_PATH%\cv.hpp %OBO_PATH%
+copy %CVGEN_PATH%\cv.cpp %OBO_PATH%