diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9a6dd074a..92652f6ad 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -86,6 +86,14 @@ jobs:
           repository: sbt/zinc
           ref: develop
           path: zinc
+      - name: Cleanup SBT server and named pipes (Windows only)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          # Kill sbt processes if any are running
+          Get-Process sbt -ErrorAction SilentlyContinue | Stop-Process -Force
+          # Remove all SBT named pipes, suppress errors if none exist
+          Remove-Item "\\.\pipe\sbt-*" -ErrorAction SilentlyContinue
       - name: Setup JDK
         uses: actions/setup-java@v5
         with:
diff --git a/main/src/main/scala/sbt/plugins/DependencyTreeSettings.scala b/main/src/main/scala/sbt/plugins/DependencyTreeSettings.scala
index 0f14c7dcb..ed47af3af 100644
--- a/main/src/main/scala/sbt/plugins/DependencyTreeSettings.scala
+++ b/main/src/main/scala/sbt/plugins/DependencyTreeSettings.scala
@@ -324,6 +324,41 @@ OPTIONS
 
   case class ArtifactPattern(organization: String, name: String, version: Option[String])
 
+  private[plugins] def createArtifactPatternParser(
+      graph: ModuleGraph
+  ): Parser[ArtifactPattern] =
+    graph.nodes
+      .map(_.id)
+      .groupBy(m => (m.organization, m.name))
+      .map { case ((org, name), modules) =>
+        // Empty versions cause parser token creation to fail
+        val versionParsers: Seq[Parser[Option[String]]] =
+          modules
+            .filter(_.version.nonEmpty)
+            .map { id =>
+              token(Space ~> id.version).?
+            }
+
+        // Handle modules with only empty versions
+        val effectiveVersionParser =
+          if versionParsers.isEmpty then success(None)
+          else oneOf(versionParsers)
+
+        (Space ~> token(org) ~ token(Space ~> name) ~ effectiveVersionParser).map {
+          case ((org, name), version) => ArtifactPattern(org, name, version)
+        }
+      }
+      .reduceOption(_ | _)
+      .getOrElse {
+        // If the dependencyTreeModuleGraphStore couldn't be loaded because no dependency tree command was run before, we should still provide a parser for the command.
+        ((Space ~> token(StringBasic, "<organization>")) ~ (Space ~> token(
+          StringBasic,
+          "<module>"
+        )) ~ (Space ~> token(StringBasic, "<version?>")).?).map { case ((org, mod), version) =>
+          ArtifactPattern(org, mod, version)
+        }
+      }
+
   val artifactPatternParser: Def.Initialize[State => Parser[ArtifactPattern]] =
     Keys.resolvedScoped { ctx => (state: State) =>
       val graph =
@@ -331,31 +366,9 @@ OPTIONS
           Nil,
           Nil
         )
-
-      graph.nodes
-        .map(_.id)
-        .groupBy(m => (m.organization, m.name))
-        .map { case ((org, name), modules) =>
-          val versionParsers: Seq[Parser[Option[String]]] =
-            modules.map { id =>
-              token(Space ~> id.version).?
-            }
-
-          (Space ~> token(org) ~ token(Space ~> name) ~ oneOf(versionParsers)).map {
-            case ((org, name), version) => ArtifactPattern(org, name, version)
-          }
-        }
-        .reduceOption(_ | _)
-        .getOrElse {
-          // If the dependencyTreeModuleGraphStore couldn't be loaded because no dependency tree command was run before, we should still provide a parser for the command.
-          ((Space ~> token(StringBasic, "<organization>")) ~ (Space ~> token(
-            StringBasic,
-            "<module>"
-          )) ~ (Space ~> token(StringBasic, "<version?>")).?).map { case ((org, mod), version) =>
-            ArtifactPattern(org, mod, version)
-          }
-        }
+      createArtifactPatternParser(graph)
     }
+
   val shouldForceParser: Parser[Boolean] =
     (Space ~> (Parser.literal("-f") | "--force")).?.map(_.isDefined)
 
diff --git a/main/src/test/scala/sbt/plugins/DependencyTreeTest.scala b/main/src/test/scala/sbt/plugins/DependencyTreeTest.scala
index 89942aecf..cb34bb14f 100644
--- a/main/src/test/scala/sbt/plugins/DependencyTreeTest.scala
+++ b/main/src/test/scala/sbt/plugins/DependencyTreeTest.scala
@@ -10,7 +10,17 @@ package sbt
 package plugins
 
 import sbt.internal.util.complete.Parser
-import DependencyTreeSettings.{ Arg, ArgsParser, Fmt, FmtParser }
+import DependencyTreeSettings.{
+  Arg,
+  ArgsParser,
+  Fmt,
+  FmtParser,
+  ArtifactPattern,
+  createArtifactPatternParser
+}
+import sbt.internal.graph.ModuleGraph
+import sbt.internal.graph.GraphModuleId
+import sbt.internal.graph.Module
 
 object DependencyTreeTest extends verify.BasicTestSuite:
   test("Parse args") {
@@ -31,6 +41,77 @@ object DependencyTreeTest extends verify.BasicTestSuite:
     assert(parseFormat("graph") == Fmt.Graph)
   }
 
+  test("ArtifactPatternParser with normal modules") {
+    val graph = ModuleGraph(
+      Seq(
+        node("org1", "name1", "1.0"),
+        node("org1", "name1", "2.0")
+      ),
+      Nil
+    )
+    val parser = createArtifactPatternParser(graph)
+
+    // Test matching
+    assert(
+      Parser.parse(" org1 name1 1.0", parser) == Right(
+        ArtifactPattern("org1", "name1", Some("1.0"))
+      )
+    )
+    assert(
+      Parser.parse(" org1 name1 2.0", parser) == Right(
+        ArtifactPattern("org1", "name1", Some("2.0"))
+      )
+    )
+    assert(Parser.parse(" org1 name1", parser) == Right(ArtifactPattern("org1", "name1", None)))
+  }
+
+  test("ArtifactPatternParser with completely empty graph") {
+    val graph = ModuleGraph.empty
+    val parser = createArtifactPatternParser(graph)
+
+    // Should fallback to generic parser
+    assert(
+      Parser.parse(" org1 name1 1.0", parser) == Right(
+        ArtifactPattern("org1", "name1", Some("1.0"))
+      )
+    )
+  }
+
+  test("ArtifactPatternParser should not throw RuntimeException on empty version") {
+    val graph = ModuleGraph(
+      Seq(
+        node("org1", "name1", "")
+      ),
+      Nil
+    )
+    // This previously threw RuntimeException: String literal cannot be empty
+    val parser = createArtifactPatternParser(graph)
+
+    // Should parse org and name, version is None
+    assert(Parser.parse(" org1 name1", parser) == Right(ArtifactPattern("org1", "name1", None)))
+  }
+
+  test("ArtifactPatternParser mixed valid and empty versions") {
+    val graph = ModuleGraph(
+      Seq(
+        node("org1", "name1", ""),
+        node("org1", "name1", "1.0")
+      ),
+      Nil
+    )
+    val parser = createArtifactPatternParser(graph)
+
+    // Valid version should be selectable
+    assert(
+      Parser.parse(" org1 name1 1.0", parser) == Right(
+        ArtifactPattern("org1", "name1", Some("1.0"))
+      )
+    )
+
+    // No version should be selectable
+    assert(Parser.parse(" org1 name1", parser) == Right(ArtifactPattern("org1", "name1", None)))
+  }
+
   def parseArgs(args: List[String]): Seq[Arg] =
     Parser.parse(" " + args.mkString(" "), ArgsParser) match
       case Right(args) => args
@@ -40,4 +121,8 @@ object DependencyTreeTest extends verify.BasicTestSuite:
     Parser.parse(fmt, FmtParser) match
       case Right(x)  => x
       case Left(err) => sys.error(err)
+
+  def node(org: String, name: String, version: String): Module =
+    Module(GraphModuleId(org, name, version), None, "", None, None, None)
+
 end DependencyTreeTest
diff --git a/sbt-app/src/sbt-test/dependency-graph/ignoreScalaLibrary/build.sbt b/sbt-app/src/sbt-test/dependency-graph/ignoreScalaLibrary/build.sbt
index 0f5889a1c..0a9848dc9 100644
--- a/sbt-app/src/sbt-test/dependency-graph/ignoreScalaLibrary/build.sbt
+++ b/sbt-app/src/sbt-test/dependency-graph/ignoreScalaLibrary/build.sbt
@@ -27,14 +27,14 @@ default:sbt_8ae1da13_2.12:0.1.0-SNAPSHOT [S]
 */
 
   val expectedGraph =
-    """default:default-e95e05_2.12:0.1-SNAPSHOT [S]
+    """foo:foo_2.12:0.1.0-SNAPSHOT [S]
       |  +-ch.qos.logback:logback-classic:1.0.7
-      |  | +-ch.qos.logback:logback-core:1.0.7
       |  | +-org.slf4j:slf4j-api:1.6.6 (evicted by: 1.7.2)
-      |  | +-org.slf4j:slf4j-api:1.7.2
       |  |
       |  +-org.slf4j:slf4j-api:1.7.2
       |  """.stripMargin
+
+
   // IO.writeLines(file("/tmp/blib"), sanitize(graph).split("\n"))
   // IO.writeLines(file("/tmp/blub"), sanitize(expectedGraph).split("\n"))
   require(sanitize(graph) == sanitize(expectedGraph), "Graph for report %s was '\n%s' but should have been '\n%s'" format (report, sanitize(graph), sanitize(expectedGraph)))
diff --git a/sbt-app/src/sbt-test/dependency-graph/whatDependsOn-without-previous-initialization/project/plugins.sbt b/sbt-app/src/sbt-test/dependency-graph/whatDependsOn-without-previous-initialization/project/plugins.sbt
index 93c66d2a9..8b1378917 100644
--- a/sbt-app/src/sbt-test/dependency-graph/whatDependsOn-without-previous-initialization/project/plugins.sbt
+++ b/sbt-app/src/sbt-test/dependency-graph/whatDependsOn-without-previous-initialization/project/plugins.sbt
@@ -1 +1 @@
-addDependencyTreePlugin
+
diff --git a/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/pending b/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/pending
index 111738e33..9bf597e6c 100644
--- a/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/pending
+++ b/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/pending
@@ -1,3 +1,3 @@
 # to initialize parser with deps
 > Compile/dependencyTreeModuleGraph0
-> check
\ No newline at end of file
+> check
diff --git a/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/project/plugins.sbt b/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/project/plugins.sbt
index 93c66d2a9..8b1378917 100644
--- a/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/project/plugins.sbt
+++ b/sbt-app/src/sbt-test/dependency-graph/whatDependsOn/project/plugins.sbt
@@ -1 +1 @@
-addDependencyTreePlugin
+