Drop user-facing support for ScipBuildTool

ScipBuildTool is now an internal worker dispatched only when the Bazel
aspect (scip_java.bzl) invokes 'scip-java index --scip-config <file>'.

User-facing changes:
- Remove 'index-dependency' subcommand.
- Hide --scip-config, --scip-ignored-javac-option-prefixes,
  --scip-ignored-annotation-processors, and --strict-compilation from
  'scip-java index --help'.
- Drop the 'SCIP Build Tool' help section and fix the misplaced
  description on --build-command.
- Stop auto-detecting lsif-java.json / scip-java.json files; the only
  supported build tools advertised to users are Maven and Gradle.
- Drop jq from the Dockerfile, Nix flake, dev-shell docs, and the
  scip-java docker wrapper (it only existed to read lsif-java.json).

Internal:
- BuildTool.autoOrdered no longer lists ScipBuildTool.
- IndexCommand.run() early-returns into ScipBuildTool when --scip-config
  is provided, keeping the Bazel aspect functional.
- ScipBuildTool.usedInCurrentDirectory() always returns false and
  parsedConfig only reads index.scipConfig.

Tests/snapshots:
- Remove ScipBuildToolSuite, TracingServer, LibrarySnapshotGenerator,
  AggregateSnapshotGenerator, SemanticdbJavacSnapshotGenerator,
  LibrarySnapshotSuite, and the org/jetbrains/exposed snapshot fixtures.
- SaveSnapshots and SnapshotSuite are simplified to only drive
  MinimizedSnapshotScipGenerator.

Author: jupblb

CONTRIBUTING.md

@@ -15,7 +15,7 @@ nix develop .#jdk21      # JDK 21
 ```
 
 This drops you into a shell with `sbt`, `cs` (coursier), `maven`, `gradle`,
-`bazelisk`, `scalafmt`, `nodejs`, `yarn`, `git`, `jq`, etc. all pinned to the
+`bazelisk`, `scalafmt`, `nodejs`, `yarn`, `git`, etc. all pinned to the
 versions used in CI.
 
 If you'd rather install tools manually, you'll need at least:
@@ -55,7 +55,6 @@ These are the main components of the project.
 | `buildTools/test`                                                   | sbt      | Run slow build tool tests (Gradle, Maven).                                          |
 | `snapshots/testOnly tests.MinimizedSnapshotSuite`                   | sbt      | Runs fast snapshot tests. Indexes a small set of files under `tests/minimized`.     |
 | `snapshots/testOnly tests.MinimizedSnapshotSuite -- *InnerClasses*` | sbt      | Runs only individual tests cases matching the name "InnerClasses".                  |
-| `snapshots/testOnly tests.LibrarySnapshotSuite`                     | sbt      | Runs slow snapshot tests. Indexes a corpus of external Java libraries.              |
 | `snapshots/test`                                                    | sbt      | Runs all snapshot tests.                                                            |
 | `snapshots/run`                                                     | sbt      | Update snapshot tests. Use this command after you have fixed a bug.                 |
 | `cli/run --cwd DIRECTORY`                                           | sbt      | Run `scip-java` command-line tool against a given Gradle/Maven build.               |

Dockerfile

@@ -1,6 +1,6 @@
 FROM eclipse-temurin:17@sha256:6eca72bb4cd5fb8cd215f2579a4dfffd24b0f47effb6c868b7e92b7f0422fa9f
 
-RUN apt-get update && apt-get install --yes jq wget curl zip unzip git python3 python3-pip autoconf automake libtool build-essential libtool make g++
+RUN apt-get update && apt-get install --yes wget curl zip unzip git python3 python3-pip autoconf automake libtool build-essential libtool make g++
 
 WORKDIR /workdir
 

bin/scip-java-docker-script.sh

@@ -4,13 +4,6 @@
 # `scip-java` binary is already installed at `/app/scip-java/bin/scip-java`.
 set -eu
 JVM_VERSION="${JVM_VERSION:-21,17,11,8}"
-FILE="$PWD/lsif-java.json"
-if test -f "$FILE"; then
-	FROM_CONFIG=$(jq -r '.jvm' "$FILE")
-	if [ "$FROM_CONFIG" != "null" ]; then
-		JVM_VERSION="$FROM_CONFIG"
-	fi
-fi
 
 JVM_VERSIONS=$(echo "$JVM_VERSION" | tr "," "\n")
 

flake.nix

@@ -27,7 +27,6 @@
               git
               (gradle.override ({ java = jdk; }))
               jdk
-              jq
               (maven.override ({ jdk_headless = jdk; }))
               nixfmt
               nodejs

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

@@ -3,7 +3,6 @@ package com.sourcegraph.scip_java
 import java.io.PrintStream
 
 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 moped.cli.Application
@@ -21,7 +20,6 @@ object ScipJava {
       CommandParser[VersionCommand],
       CommandParser[IndexCommand],
       CommandParser[IndexSemanticdbCommand],
-      CommandParser[IndexDependencyCommand],
       CommandParser[SnapshotCommand]
     )
   )

scip-java/src/main/scala/com/sourcegraph/scip_java/buildtools/BuildTool.scala

@@ -27,8 +27,6 @@ object BuildTool {
     // first detected build tool will be used in `auto` mode
     // Bazel is missing because it isn't supported by auto-indexing
 
-    // first as it indicates user's intent to use SCIP auto-indexing
-    new ScipBuildTool(index),
     // Maven first, then Gradle
     // To match the order indicated in IntelliJ Java developer survey 2022:
     // https://www.jetbrains.com/lp/devecosystem-2022/java/#which-build-systems-do-you-regularly-use-if-any-

scip-java/src/main/scala/com/sourcegraph/scip_java/buildtools/ScipBuildTool.scala

@@ -57,16 +57,27 @@ import os.ProcessOutput.Readlines
 import os.SubprocessException
 
 /**
- * A custom build tool that is specifically made for scip-java.
+ * Internal build-tool worker used exclusively by the Bazel aspect.
  *
- * The purpose of this build tool is to SCIP index the source code inside
- * `*-sources.jar` files of Maven dependencies. Builds are written in a JSON
- * file with the following format:
+ * This tool is no longer part of the user-facing build-tool auto-detection
+ * surface (see [[BuildTool.autoOrdered]]). It is dispatched directly from
+ * [[com.sourcegraph.scip_java.commands.IndexCommand]] when the hidden
+ * `--scip-config` flag is provided, which is how the Bazel aspect
+ * (`scip_java.bzl`) invokes per-target indexing.
+ *
+ * The aspect generates a JSON file per Bazel target with the following
+ * shape and passes its path via `--scip-config`:
  *
  * {{{
  *   {
- *     "dependencies": ["junit:junit:4.13.1"],
- *     "jvm": "11"
+ *     "javaHome": "/path/to/jdk",
+ *     "classpath": [...],
+ *     "sourceFiles": [...],
+ *     "javacOptions": [...],
+ *     "jvmOptions": [...],
+ *     "processors": [...],
+ *     "processorpath": [...],
+ *     "bootclasspath": [...]
  *   }
  * }}}
  */
@@ -83,9 +94,10 @@ class ScipBuildTool(index: IndexCommand) extends BuildTool("SCIP", index) {
     .getPathMatcher("glob:**.{java,kt}")
   private val moduleInfo = Paths.get("module-info.java")
 
-  override def usedInCurrentDirectory(): Boolean = configFiles.exists(path =>
-    Files.isRegularFile(path)
-  )
+  // ScipBuildTool is dispatched directly from IndexCommand.run() when
+  // --scip-config is provided, so it does not participate in build-tool
+  // auto-detection.
+  override def usedInCurrentDirectory(): Boolean = false
   override def isHidden: Boolean = true
   override def generateScip(): Int = {
     BuildTool.generateScipFromTargetroot(
@@ -97,11 +109,6 @@ class ScipBuildTool(index: IndexCommand) extends BuildTool("SCIP", index) {
 
   private def targetroot: Path = index.finalTargetroot(defaultTargetroot)
   private def defaultTargetroot: Path = Paths.get("target")
-  private def configFiles =
-    index.scipConfig.toList ++
-      ScipBuildTool
-        .ConfigFileNames
-        .map(name => index.workingDirectory.resolve(name))
   private def generateSemanticdb(): CommandResult = {
     parsedConfig match {
       case ValueResult(value) =>
@@ -125,14 +132,13 @@ class ScipBuildTool(index: IndexCommand) extends BuildTool("SCIP", index) {
     }
   }
 
-  /** Parses the lsif-java.json file into a Config object. */
+  /** Parses the --scip-config file into a Config object. */
   private def parsedConfig: Result[Config] = {
-    configFiles.find(path => Files.isRegularFile(path)) match {
+    index.scipConfig.filter(Files.isRegularFile(_)) match {
       case None =>
         ErrorResult(
           Diagnostic.error(
-            s"no config file found. To fix this problem, create a config file in the path '${configFiles
-                .head}'"
+            s"no --scip-config file found at '${index.scipConfig.map(_.toString).getOrElse("")}'"
           )
         )
       case Some(configFile) =>
@@ -635,7 +641,7 @@ class ScipBuildTool(index: IndexCommand) extends BuildTool("SCIP", index) {
   }
 
   /**
-   * Gets parsed from "junit:junit:4.13.1" strings inside lsif-java.json files.
+   * Gets parsed from "junit:junit:4.13.1" strings inside --scip-config files.
    */
   private case class Dependency(
       groupId: String = "",
@@ -682,7 +688,7 @@ class ScipBuildTool(index: IndexCommand) extends BuildTool("SCIP", index) {
       }
   }
 
-  /** Gets parsed from lsif-java.json files. */
+  /** Gets parsed from --scip-config files. */
   private case class Config(
       reportWarningOnEmptyIndex: Boolean = true,
       javaHome: Option[String] = None,
@@ -704,14 +710,6 @@ class ScipBuildTool(index: IndexCommand) extends BuildTool("SCIP", index) {
 }
 
 object ScipBuildTool {
-  // This file is named "lsif-java.json" instead of "scip-java.json" in order to
-  // preserve compatibility with "JVM dependencies" repos
-  // (https://docs.sourcegraph.com/integration/jvm). If we rename to
-  // "scip-java.json" then the git commit SHAs of these repos changes and old
-  // canonical URLs will become 404 links. The lsif-java.json file is not
-  // supposed to be written by end-users anyways. It's mostly an implementation
-  // default for how we support cross-repo navigation with scip-java.
-  val ConfigFileNames = List("scip-java.json", "lsif-java.json")
   val isIgnoredAnnotationProcessor = Set(
     "org.openjdk.jmh.generators.BenchmarkProcessor"
   )

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

@@ -56,20 +56,11 @@ case class IndexCommand(
     packagehub: Option[String] = None,
     @Hidden // Hidden because it's only used for testing purposes
     temporaryDirectory: Option[Path] = None,
-    @Section("SCIP Build Tool")
-    @Description(
-      "List of Java compiler option prefixes that should be excluded from compilation during indexing. " +
-        "This flag is only used when indexing via scip-java.json files or Bazel."
-    )
+    @Hidden // Internal flag used by the Bazel aspect to pass per-target build configuration.
     scipIgnoredJavacOptionPrefixes: List[String] = Nil,
-    @Description(
-      "List of fully qualified annotation processors that should be ignored when indexing a codebase. " +
-        "This flag is only used when indexing via scip-java.json files or Bazel."
-    )
+    @Hidden // Internal flag used by the Bazel aspect to pass per-target build configuration.
     scipIgnoredAnnotationProcessors: List[String] = Nil,
-    @Description(
-      "Path to a scip-java.json file with build configuration. By default, the path scip-java.json is used."
-    )
+    @Hidden // Internal flag used by the Bazel aspect to pass per-target build configuration.
     scipConfig: Option[Path] = None,
     @Section("Bazel")
     @Description(
@@ -86,15 +77,14 @@ case class IndexCommand(
       "If true, automatically tries to extract the printed out sandbox command and re-run the command to reveal the underlying problem."
     )
     bazelAutorunSandboxCommand: Boolean = true,
+    @Hidden
+    @Description("Fail command invocation if compiler produces any errors")
+    strictCompilation: Boolean = false,
     @Description(
       "Optional. The build command to use to compile all sources. " +
         "Defaults to a build-specific command. For example, the default command for Maven command is 'clean verify -DskipTests'." +
         "To override the default, pass in the build command after a double dash: 'scip-java index -- compile test:compile'"
     )
-
-    @Hidden
-    @Description("Fail command invocation if compiler produces any errors")
-    strictCompilation: Boolean = false,
     @TrailingArguments()
     buildCommand: List[String] = Nil,
     @Hidden
@@ -152,6 +142,14 @@ case class IndexCommand(
       buildCommand
 
   override def run(): Int = {
+    // The Bazel aspect invokes `scip-java index --scip-config <file>` for
+    // every Java target it discovers. When --scip-config is provided we
+    // bypass build-tool auto-detection entirely and dispatch directly to
+    // the internal ScipBuildTool worker.
+    if (scipConfig.isDefined) {
+      return new ScipBuildTool(this).generateScip()
+    }
+
     val allBuildTools = BuildTool.all(this)
     val usedBuildTools = allBuildTools.filter(_.usedInCurrentDirectory())
     val matchingBuildTools = usedBuildTools.filter(tool =>
@@ -172,17 +170,13 @@ case class IndexCommand(
             unknownBuildTool(buildTool, usedBuildTools)
           case tool :: Nil =>
             tool.generateScip()
-          case many @ (first :: rest) =>
-            if (first.isInstanceOf[ScipBuildTool] && scipConfig.isDefined) {
-              first.generateScip()
-            } else {
-              val names = many.map(_.name).mkString(", ")
-              app.error(
-                s"Multiple build tools detected: $names. " +
-                  s"To fix this problem, use the '--build-tool=BUILD_TOOL_NAME' flag to specify which build tool to run."
-              )
-              1
-            }
+          case many =>
+            val names = many.map(_.name).mkString(", ")
+            app.error(
+              s"Multiple build tools detected: $names. " +
+                s"To fix this problem, use the '--build-tool=BUILD_TOOL_NAME' flag to specify which build tool to run."
+            )
+            1
         }
     }
   }