Skyline has at least one checked in devtools "bin" folder, don't stom…

…p if contents are source controlled (#3239)

Refactored clean-apps.bat to preserve source controlled files in obj/ and bin/ subdirs that would formerly have been deleted, causing an annoying and unnecessary dirty repo situation.

Also, now cleaning everything under pwiz_tools/Shared instead of just selected subdirs of Shared - some subdirs have been recently added there without being noted in clean-apps.bat, and devs really shouldn't have to worry about that.

Internal build issue, not reported by any user

pwiz_tools/clean-apps.bat

@@ -8,17 +8,10 @@ set PWIZ_ROOT=%PWIZ_ROOT:~0,-1%
 pushd %PWIZ_ROOT%
 
 echo   Cleaning .NET applications...
-for /d /r Shared\BiblioSpec %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Shared\Common %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Shared\CommonTest %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Shared\Crawdad %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Shared\MSGraph %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Shared\ProteomeDb %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Shared\ProteowizardWrapper %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Shared\zedgraph %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r Skyline %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r SeeMS %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
-for /d /r MSConvertGUI %%d in (obj, bin) do @if exist "%%d" rmdir /s/q "%%d"
+call :CleanBinaries Shared
+call :CleanBinaries Skyline
+call :CleanBinaries SeeMS
+call :CleanBinaries MSConvertGUI
 
 IF EXIST Shared\CommonTest rmdir /s/q Shared\CommonTest
 
@@ -27,3 +20,31 @@ IF EXIST Skyline\CleanSkyline.bat call Skyline\CleanSkyline.bat
 IF EXIST BiblioSpec\CleanBiblioSpec.bat call BiblioSpec\CleanBiblioSpec.bat
 
 popd
+rem Exit the script
+exit /b
+
+
+REM subroutine for cleaning out obj and bin dirs, but avoiding any source controlled files
+:CleanBinaries
+rem %~1 - The directory to clean
+if not exist "%~1" exit /b
+
+rem Iterate through all files and directories in the current directory
+for /d /r %~1 %%d in (obj, bin) do (
+    if exist "%%d" (
+        pushd "%%d" >nul
+        rem Check if the directory contains files tracked by Git (error 1 if not)
+        git ls-files --error-unmatch . >nul 2>&1
+        if errorlevel 1 (
+            REM contains no source controlled files, delete directory
+            popd >nul
+            rmdir /s /q "%%d"
+        ) else (
+            REM remove any non-source-controlled files
+            git clean -f -q
+            popd >nul
+        )
+    )
+)
+exit /b
+REM end of subroutine