Bump Boogie dependency to v3.1.3 (#5190)

### Description

Bump Boogie dependency to v3.1.3

This most importantly includes
boogie-org/boogie#859

### How has this been tested?

Existing tests should be sufficient.

By submitting this pull request, I confirm that my contribution is made
under the terms of the MIT license.

Source/DafnyCore/DafnyCore.csproj

@@ -34,7 +34,7 @@
       <PackageReference Include="System.CommandLine" Version="2.0.0-beta4.22272.1" />
       <PackageReference Include="System.Runtime.Numerics" Version="4.3.0" />
       <PackageReference Include="System.Collections.Immutable" Version="1.7.1" />
-      <PackageReference Include="Boogie.ExecutionEngine" Version="3.1.2" />
+      <PackageReference Include="Boogie.ExecutionEngine" Version="3.1.3" />
       <PackageReference Include="Tomlyn" Version="0.16.2" />
   </ItemGroup>
 

customBoogie.patch

@@ -61,7 +61,7 @@ index 4a8b2f89b..a308be9bf 100644
        <PackageReference Include="System.CommandLine" Version="2.0.0-beta4.22272.1" />
        <PackageReference Include="System.Runtime.Numerics" Version="4.3.0" />
        <PackageReference Include="System.Collections.Immutable" Version="1.7.1" />
--      <PackageReference Include="Boogie.ExecutionEngine" Version="3.1.2" />
+-      <PackageReference Include="Boogie.ExecutionEngine" Version="3.1.3" />
 +      <ProjectReference Include="..\..\boogie\Source\ExecutionEngine\ExecutionEngine.csproj" />
 +      <ProjectReference Include="..\..\boogie\Source\BaseTypes\BaseTypes.csproj" />
 +      <ProjectReference Include="..\..\boogie\Source\Core\Core.csproj" />

docs/DafnyRef/Options.txt

@@ -646,6 +646,11 @@ Usage: dafny [ option ... ] [ filename ... ]
                 report. This generalizes and replaces the previous
                 (undocumented) `/printNecessaryAssertions` option.
 
+  /keepQuantifier
+                If pool-based quantifier instantiation creates instances of a quantifier
+                then keep the quantifier along with the instances. By default, the quantifier
+                is dropped if any instances are created.
+
   ---- Verification-condition splitting --------------------------------------
 
   /vcsMaxCost:<f>

dotnet-tools.json

@@ -9,7 +9,7 @@
       ]
     },
     "boogie": {
-      "version": "3.1.2",
+      "version": "3.1.3",
       "commands": [
         "boogie"
       ]