ProteoWizard · brendanx67 · Oct 20, 2025 · Oct 19, 2025 · Oct 19, 2025 · Oct 19, 2025
diff --git a/.editorconfig b/.editorconfig
@@ -1,4 +1,4 @@
-[*.cs]
+[*.cs]
 
 # IDE0011: Add braces
 csharp_prefer_braces = true
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,4 @@
+{
+    "dotnet.preferCSharpExtension": true,
+    "dotnet.defaultSolution": "pwiz_tools/Skyline/Skyline.sln"
+}
diff --git a/ThermoMethod.bat b/ThermoMethod.bat
@@ -0,0 +1 @@
+C:\proj\review\pwiz_tools\Skyline\bin\x64\Debug\Method\Thermo\BuildThermoMethod.exe -t -m "E:\test\20250212_ThermoMethod\ThoriumMethod\60SPD_PQ500PRTC_ToAlignTemplate.meth" "E:\test\20250212_ThermoMethod\ThoriumMethod\13xjtwsa.qkw\transitions.txt"
diff --git a/WORKFLOW.md b/WORKFLOW.md
@@ -226,6 +226,8 @@ The TODO file in todos/active/ contains full context. Please read it first, then
 
 ## Branch Lifecycle Workflows
 
+**IMPORTANT**: All TODO files in `todos/` are Git-tracked. Always use Git commands (`git mv`, `git add`, `git commit`) when creating, moving, or modifying TODO files. Using regular file system operations (PowerShell `Move-Item`, bash `mv`, etc.) will not properly track changes in Git history.
+
 ### Workflow 1: Creating Branch from Backlog TODO
 
 When you have a branch-ready TODO file (e.g., `todos/backlog/TODO-utf8_no_bom.md`):
@@ -237,13 +239,10 @@ git pull origin master
 git checkout -b Skyline/work/20251015_utf8_no_bom  # Use today's date
 ```
 
-**Step 2: Move and rename TODO file with date**
+**Step 2: Move and rename TODO file with Git**
 ```bash
-# On Windows (PowerShell)
-Move-Item todos\backlog\TODO-utf8_no_bom.md todos\active\TODO-20251015_utf8_no_bom.md
-
-# On Linux/Mac
-mv todos/backlog/TODO-utf8_no_bom.md todos/active/TODO-20251015_utf8_no_bom.md
+# IMPORTANT: Use git mv to preserve Git history when moving tracked files
+git mv todos/backlog/TODO-utf8_no_bom.md todos/active/TODO-20251015_utf8_no_bom.md
 ```
 
 **Step 3: Update TODO file header**
@@ -308,15 +307,10 @@ git commit -m "Add completion summary to TODO"
 git push
 ```
 
-**Step 2: Move TODO to completed/**
+**Step 2: Move TODO to completed/ with Git**
 ```bash
-# On Windows (PowerShell)
-Move-Item todos\active\TODO-YYYYMMDD_description.md todos\completed\TODO-YYYYMMDD_description.md
-
-# On Linux/Mac
-mv todos/active/TODO-YYYYMMDD_description.md todos/completed/TODO-YYYYMMDD_description.md
-
-git add todos/
+# IMPORTANT: Use git mv to preserve Git history when moving tracked files
+git mv todos/active/TODO-YYYYMMDD_description.md todos/completed/TODO-YYYYMMDD_description.md
 git commit -m "Move TODO to completed - ready for merge"
 git push
 ```

diff --git a/pwiz.sln b/pwiz.sln
@@ -1,4 +1,4 @@
-
+
 Microsoft Visual Studio Solution File, Format Version 12.00
 # Visual Studio 15
 VisualStudioVersion = 15.0.27703.2026

diff --git a/pwiz.vcxproj b/pwiz.vcxproj
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <Project DefaultTargets="Build" ToolsVersion="15.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <ItemGroup Label="ProjectConfigurations">
     <ProjectConfiguration Include="BrowseOnly|Win32">

diff --git a/pwiz.vcxproj.filters b/pwiz.vcxproj.filters
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <ItemGroup>
     <ClCompile Include="libraries\boost_aux\libs\nowide\src\iostream.cpp" />

diff --git a/pwiz/utility/bindings/CLI/example/pwizCLI.csproj b/pwiz/utility/bindings/CLI/example/pwizCLI.csproj
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <Project DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003" ToolsVersion="12.0">
   <PropertyGroup>
     <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>

diff --git a/pwiz/utility/bindings/CLI/example/pwizCLI.sln b/pwiz/utility/bindings/CLI/example/pwizCLI.sln
@@ -1,4 +1,4 @@
-
+
 Microsoft Visual Studio Solution File, Format Version 12.00
 # Visual Studio 2013
 VisualStudioVersion = 12.0.30110.0

diff --git a/pwiz/utility/misc/VendorReaderTestHarness.cpp b/pwiz/utility/misc/VendorReaderTestHarness.cpp
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 //

diff --git a/pwiz_aux/msrc/utility/vendor_api/Bruker/Interop.EDAL.SxS.manifest.dummy b/pwiz_aux/msrc/utility/vendor_api/Bruker/Interop.EDAL.SxS.manifest.dummy
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <!-- $Id$ -->
 <assembly xsi:schemaLocation="urn:schemas-microsoft-com:asm.v1 assembly.adaptive.xsd" manifestVersion="1.0" xmlns:asmv1="urn:schemas-microsoft-com:asm.v1" xmlns:asmv2="urn:schemas-microsoft-com:asm.v2" xmlns:asmv3="urn:schemas-microsoft-com:asm.v3" xmlns:dsig="http://www.w3.org/2000/09/xmldsig#" xmlns:co.v1="urn:schemas-microsoft-com:clickonce.v1" xmlns="urn:schemas-microsoft-com:asm.v1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
   <assemblyIdentity name="Interop.EDAL.SxS" version="1.0.0.0" type="win32" />

diff --git a/pwiz_aux/msrc/utility/vendor_api/Bruker/Interop.HSREADWRITELib.SxS.manifest.dummy b/pwiz_aux/msrc/utility/vendor_api/Bruker/Interop.HSREADWRITELib.SxS.manifest.dummy
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <!-- $Id$ -->
 <assembly xsi:schemaLocation="urn:schemas-microsoft-com:asm.v1 assembly.adaptive.xsd" manifestVersion="1.0" xmlns:asmv1="urn:schemas-microsoft-com:asm.v1" xmlns:asmv2="urn:schemas-microsoft-com:asm.v2" xmlns:asmv3="urn:schemas-microsoft-com:asm.v3" xmlns:dsig="http://www.w3.org/2000/09/xmldsig#" xmlns:co.v1="urn:schemas-microsoft-com:clickonce.v1" xmlns="urn:schemas-microsoft-com:asm.v1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
   <assemblyIdentity name="Interop.HSREADWRITELib.SxS" version="1.0.0.0" type="win32" />

diff --git a/pwiz_aux/msrc/utility/vendor_api/Shimadzu/ShimadzuReader.cpp b/pwiz_aux/msrc/utility/vendor_api/Shimadzu/ShimadzuReader.cpp
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 //

diff --git a/pwiz_aux/msrc/utility/vendor_api/UNIFI/UnifiData.cpp b/pwiz_aux/msrc/utility/vendor_api/UNIFI/UnifiData.cpp
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 //

diff --git a/pwiz_aux/msrc/utility/vendor_api/thermo/x86/fileio.manifest b/pwiz_aux/msrc/utility/vendor_api/thermo/x86/fileio.manifest
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <assembly xmlns="urn:schemas-microsoft-com:asm.v1" manifestVersion="1.0">
   <trustInfo xmlns="urn:schemas-microsoft-com:asm.v3">
     <security>

diff --git a/pwiz_tools/BiblioSpec/Navigation_only_will_not_build.sln b/pwiz_tools/BiblioSpec/Navigation_only_will_not_build.sln
@@ -1,4 +1,4 @@
-
+
 Microsoft Visual Studio Solution File, Format Version 12.00
 # Visual Studio Version 17
 VisualStudioVersion = 17.7.34009.444

diff --git a/pwiz_tools/BiblioSpec/Navigation_only_will_not_build.vcxproj b/pwiz_tools/BiblioSpec/Navigation_only_will_not_build.vcxproj
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <ItemGroup Label="ProjectConfigurations">
     <ProjectConfiguration Include="BlibBuild|x64">

diff --git a/pwiz_tools/BiblioSpec/Navigation_only_will_not_build.vcxproj.filters b/pwiz_tools/BiblioSpec/Navigation_only_will_not_build.vcxproj.filters
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <ItemGroup>
     <Filter Include="Source Files">

diff --git a/pwiz_tools/BiblioSpec/src/modifications.xml b/pwiz_tools/BiblioSpec/src/modifications.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <modifications xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <modification title="Acetyl (K)" description="Acetylation" create_date="2010-01-19T13:25:24.82357+01:00" last_modified_date="2010-01-19T14:15:40.2445414+01:00" user="neuhause" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" reporterCorrectionType="false" composition="C(2) H(2) O">
       <position>notCterm</position>

diff --git a/pwiz_tools/BiblioSpec/tests/inputs/heavy-label-modifications.xml b/pwiz_tools/BiblioSpec/tests/inputs/heavy-label-modifications.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <modifications xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <modification title="Acetyl (K)" description="Acetylation" create_date="2010-01-19T04:25:24.82357-08:00" last_modified_date="2010-01-19T05:15:40.2445414-08:00" user="neuhause" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" reporterCorrectionType="false" composition="C(2) H(2) O">
       <position>notCterm</position>

diff --git a/pwiz_tools/BiblioSpec/tests/inputs/mqpar1.xml b/pwiz_tools/BiblioSpec/tests/inputs/mqpar1.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <MaxQuantParams xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" runOnCluster="false" processFolder="M:\InstrumentQCs\BroadInst-QE2-Galileo\20130122\combined\proc">
    <rawFileInfo>
       <filePaths>

diff --git a/pwiz_tools/BiblioSpec/tests/inputs/test-mq3-modifications.local.xml b/pwiz_tools/BiblioSpec/tests/inputs/test-mq3-modifications.local.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <modifications xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <modification title="ETFPQQPPSSQQQQPL" description="LMW peptide" create_date="2018-09-20T10:33:44.2704122+02:00" last_modified_date="2018-09-20T10:34:41.5026749+02:00" user="AK Biopolymere" reporterCorrectionM2="0" reporterCorrectionM1="0" reporterCorrectionP1="0" reporterCorrectionP2="0" reporterCorrectionType="false" composition="H(119) O(28) N(21) C(80)">
       <position>anywhere</position>

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash.sln b/pwiz_tools/Bumbershoot/bumberdash/BumberDash.sln
@@ -1,4 +1,4 @@
-
+
 Microsoft Visual Studio Solution File, Format Version 11.00
 # Visual Studio 2010
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{7EE15627-F98C-40F5-ACE0-C17E261E029D}"

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash.vsmdi b/pwiz_tools/Bumbershoot/bumberdash/BumberDash.vsmdi
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <TestLists xmlns="http://microsoft.com/schemas/VisualStudio/TeamTest/2010">
   <TestList name="Lists of Tests" id="8c43106b-9dc1-4907-a29f-aa66a61bf5b6">
     <RunConfiguration id="1ff74241-afc5-4e9c-a2bf-bcb6c7eb42c6" name="Local Test Run" storage="localtestrun.testrunconfig" type="Microsoft.VisualStudio.TestTools.Common.TestRunConfiguration, Microsoft.VisualStudio.QualityTools.Common,   PublicKeyToken=b03f5f7f11d50a3a" />

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/BumberDash.csproj b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/BumberDash.csproj
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <PropertyGroup>
     <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/CometHandler.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/CometHandler.cs
@@ -1,4 +1,4 @@
-using System;
+using System;
 using System.Collections.Generic;
 using System.Globalization;
 using System.IO;

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/AddJobForm.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/AddJobForm.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/AddJobForm.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/AddJobForm.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigForm.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigForm.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigForm.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigForm.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigWizard.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigWizard.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigWizard.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigWizard.cs
@@ -1,4 +1,4 @@
-using System;
+using System;
 using System.Collections.Generic;
 using System.ComponentModel;
 using System.Data;

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigWizard.resx b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ConfigWizard.resx
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <root>
   <!-- 
     Microsoft ResX Schema 

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ImportTemplateForm.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ImportTemplateForm.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ImportTemplateForm.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/ImportTemplateForm.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/LogForm.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/LogForm.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/LogForm.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/LogForm.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/QueueForm.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/QueueForm.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/QueueForm.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/QueueForm.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/TextPromptBox.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/TextPromptBox.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/TextPromptBox.designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Forms/TextPromptBox.designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/MSGFHandler.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/MSGFHandler.cs
@@ -1,4 +1,4 @@
-using System;
+using System;
 using System.Collections.Generic;
 using System.Globalization;
 using System.Linq;

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Model/DataModel.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Model/DataModel.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Model/DataModel.hbm.xml b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Model/DataModel.hbm.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8" ?>
+<?xml version="1.0" encoding="utf-8" ?>
 <hibernate-mapping xmlns="urn:nhibernate-mapping-2.2"
                    assembly ="BumberDash"
                    namespace ="BumberDash.Model">

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Model/SessionManager.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Model/SessionManager.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Program.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Program.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/ProgramHandler.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/ProgramHandler.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id: ProgramHandler.cs 115 2013-08-13 13:54:51Z holmanjd $
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Resources.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Resources.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Resources.resx b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Resources.resx
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <root>
   <!-- 
     Microsoft ResX Schema 

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Settings.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Settings.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Settings.settings b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Properties/Settings.settings
@@ -1,4 +1,4 @@
-<?xml version='1.0' encoding='utf-8'?>
+<?xml version='1.0' encoding='utf-8'?>
 <SettingsFile xmlns="http://schemas.microsoft.com/VisualStudio/2004/01/settings" CurrentProfile="(Default)" GeneratedClassNamespace="BumberDash.Properties" GeneratedClassName="Settings">
   <Profiles />
   <Settings>

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Util.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/Util.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id: Util.cs 107 2012-11-10 01:07:43Z chambm $
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/app.config b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/app.config
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0"?>
 <configuration>
     <configSections>
         <sectionGroup name="userSettings" type="System.Configuration.UserSettingsGroup, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" >

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/lib/DataGridViewProgressBar.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/lib/DataGridViewProgressBar.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 //

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/lib/ProgramHandler.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/lib/ProgramHandler.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/BumberDash/lib/Util.cs b/pwiz_tools/Bumbershoot/bumberdash/BumberDash/lib/Util.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id$
 //
 // The contents of this file are subject to the Mozilla Public License

diff --git a/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/BreadCrumbControl.Designer.cs b/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/BreadCrumbControl.Designer.cs
diff --git a/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/BreadCrumbControl.cs b/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/BreadCrumbControl.cs
@@ -1,4 +1,4 @@
-//
+//
 // $Id: BreadCrumbControl.cs 55 2011-04-28 15:57:33Z chambm $
 //
 //

diff --git a/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/BreadCrumbControl.resx b/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/BreadCrumbControl.resx
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <root>
   <!-- 
     Microsoft ResX Schema 

diff --git a/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/CustomDataSourceDialog.csproj b/pwiz_tools/Bumbershoot/bumberdash/CustomDataSourceDialog/CustomDataSourceDialog.csproj
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <Project ToolsVersion="4.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
   <PropertyGroup>
     <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		C:\proj\review\pwiz_tools\Skyline\bin\x64\Debug\Method\Thermo\BuildThermoMethod.exe -t -m "E:\test\20250212_ThermoMethod\ThoriumMethod\60SPD_PQ500PRTC_ToAlignTemplate.meth" "E:\test\20250212_ThermoMethod\ThoriumMethod\13xjtwsa.qkw\transitions.txt"
-Original file line number
+Diff line change
@@ -1,4 +1,4 @@
-    //
+    //
     // $Id$
     //
     //
@@ Expand Down @@