Remove LSIF graph format support

Drop support for LSIF output format, keeping only typed SCIP output
(.scip and .scip.ndjson).

Deleted:
- lsif.proto and generated types (LsifObject, LsifPosition, LsifHover, etc.)
- SnapshotLsifCommand (was already deprecated)
- MarkupContent, ResultIds, ResultSets, ScipByteOutputStream

Simplified:
- ScipOutputFormat: removed GRAPH_NDJSON/GRAPH_PROTOBUF
- ScipWriter: removed 18 LSIF graph emission methods
- ScipOutputStream: simplified to raw byte writing
- ScipSemanticdb: removed runGraph() code path
- ScipSemanticdbOptions: LsifToolInfo -> Scip.ToolInfo
- PackageTable: removed ScipWriter dependency

Author: jupblb

scip-java/src/main/scala/com/sourcegraph/scip_java/ScipJava.scala

@@ -6,7 +6,6 @@ import com.sourcegraph.scip_java.commands.IndexCommand
 import com.sourcegraph.scip_java.commands.IndexDependencyCommand
 import com.sourcegraph.scip_java.commands.IndexSemanticdbCommand
 import com.sourcegraph.scip_java.commands.SnapshotCommand
-import com.sourcegraph.scip_java.commands.SnapshotLsifCommand
 import moped.cli.Application
 import moped.cli.CommandParser
 import moped.commands.HelpCommand
@@ -23,8 +22,7 @@ object ScipJava {
       CommandParser[IndexCommand],
       CommandParser[IndexSemanticdbCommand],
       CommandParser[IndexDependencyCommand],
-      CommandParser[SnapshotCommand],
-      CommandParser[SnapshotLsifCommand]
+      CommandParser[SnapshotCommand]
     )
   )
   def main(args: Array[String]): Unit = {

scip-java/src/main/scala/com/sourcegraph/scip_java/commands/IndexSemanticdbCommand.scala

@@ -7,7 +7,7 @@ import java.util.concurrent.TimeUnit
 import scala.jdk.CollectionConverters._
 
 import com.sourcegraph.io.AbsolutePath
-import com.sourcegraph.lsif_protocol.LsifToolInfo
+import com.sourcegraph.Scip
 import com.sourcegraph.scip_java.BuildInfo
 import com.sourcegraph.scip_java.buildtools.ClasspathEntry
 import com.sourcegraph.scip_semanticdb.ConsoleScipSemanticdbReporter
@@ -79,7 +79,7 @@ final case class IndexSemanticdbCommand(
     if (format == ScipOutputFormat.UNKNOWN) {
       app.error(
         s"unknown output format for filename '$outputFilename'. " +
-          s"Supported file extension are `*.scip`, `*scip '"
+          s"Supported file extensions are `*.scip` and `*.scip.ndjson`"
       )
       return 1
     }
@@ -97,7 +97,8 @@ final case class IndexSemanticdbCommand(
         AbsolutePath.of(output, sourceroot),
         sourceroot,
         reporter,
-        LsifToolInfo
+        Scip
+          .ToolInfo
           .newBuilder()
           .setName("scip-java")
           .setVersion(BuildInfo.version)

scip-java/src/main/scala/com/sourcegraph/scip_java/commands/SnapshotLsifCommand.scala

@@ -1,7 +1,7 @@
 package com.sourcegraph.scip_semanticdb;
 
 import com.sourcegraph.scip_java.Bazelbuild;
-import com.sourcegraph.lsif_protocol.LsifToolInfo;
+import com.sourcegraph.Scip;
 
 import java.io.*;
 import java.nio.file.FileSystems;
@@ -58,7 +58,7 @@ public boolean hasErrors() {
             options.output,
             options.sourceroot,
             reporter,
-            LsifToolInfo.newBuilder().setName("scip-java").setVersion("HEAD").build(),
+            Scip.ToolInfo.newBuilder().setName("scip-java").setVersion("HEAD").build(),
             "java",
             ScipOutputFormat.TYPED_PROTOBUF,
             options.parallel,

scip-semanticdb/src/main/java/com/sourcegraph/scip_semanticdb/BazelBuildTool.java

@@ -12,28 +12,24 @@
 import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.function.Function;
+
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
 import java.util.regex.Pattern;
 
-public class PackageTable implements Function<Package, Integer> {
+public class PackageTable {
 
   private final Map<String, Package> byClassfile = new HashMap<>();
   private final Set<String> cachedJdkSymbols = new HashSet<>();
-  private final Map<Package, Integer> scip = new ConcurrentHashMap<>();
   private final JavaVersion javaVersion;
-  private final ScipWriter writer;
   private final boolean indexDirectoryEntries;
 
   private static final PathMatcher CLASS_PATTERN =
       FileSystems.getDefault().getPathMatcher("glob:**.class");
   private static final PathMatcher JAR_PATTERN =
       FileSystems.getDefault().getPathMatcher("glob:**.jar");
 
-  public PackageTable(ScipSemanticdbOptions options, ScipWriter writer) throws IOException {
-    this.writer = writer;
+  public PackageTable(ScipSemanticdbOptions options) throws IOException {
     this.javaVersion = new JavaVersion();
     this.indexDirectoryEntries = options.allowExportingGlobalSymbolsFromDirectoryEntries;
     // NOTE: it's important that we index the JDK before maven packages. Some maven packages
@@ -46,11 +42,6 @@ public PackageTable(ScipSemanticdbOptions options, ScipWriter writer) throws IOE
     }
   }
 
-  public void writeMonikerPackage(int monikerId, Package pkg) {
-    int pkgId = scip.computeIfAbsent(pkg, this);
-    writer.emitPackageInformationEdge(monikerId, pkgId);
-  }
-
   public Optional<Package> packageForSymbol(String symbol) {
     return SymbolDescriptor.toplevel(symbol)
         .flatMap(
@@ -148,9 +139,4 @@ private void indexBootstrapClasspath() throws IOException {
       }
     }
   }
-
-  @Override
-  public Integer apply(Package pkg) {
-    return writer.emitpackageinformationVertex(pkg);
-  }
 }

scip-semanticdb/src/main/java/com/sourcegraph/scip_semanticdb/MarkupContent.java

@@ -1,28 +1,20 @@
 package com.sourcegraph.scip_semanticdb;
 
-/**
- * Whether to generate index.scip (JSON) or index.scip-protobuf (Protobuf).
- *
- * <p>The Protobuf format is experimental and currently only exists as a proof-of-concept.
- */
+/** Whether to generate index.scip (Protobuf) or index.scip.ndjson (newline-delimited JSON). */
 public enum ScipOutputFormat {
-  GRAPH_NDJSON,
-  GRAPH_PROTOBUF,
   TYPED_PROTOBUF,
   TYPED_NDJSON,
   UNKNOWN;
 
   public boolean isTyped() {
-    return this == TYPED_NDJSON || this == TYPED_PROTOBUF;
+    return this != UNKNOWN;
   }
 
   public boolean isNewlineDelimitedJSON() {
-    return this == GRAPH_NDJSON || this == TYPED_NDJSON;
+    return this == TYPED_NDJSON;
   }
 
   public static ScipOutputFormat fromFilename(String name) {
-    if (name.endsWith(".lsif")) return GRAPH_NDJSON;
-    if (name.endsWith(".lsif-protobuf")) return GRAPH_PROTOBUF;
     if (name.endsWith(".scip")) return TYPED_PROTOBUF;
     if (name.endsWith(".scip.ndjson")) return TYPED_NDJSON;
     return UNKNOWN;