Fix plugin bootstrap dependency tree population (#9963)

This patch fixes a bug where the dependency tree used for classpath joining,
wasn't built using the bootstrap dependencies, for plugin bootstrappers.

patches/server/Paper-Plugins.patch

@@ -272,7 +272,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +import io.papermc.paper.plugin.entrypoint.classloader.group.SpigotPluginClassLoaderGroup;
 +import io.papermc.paper.plugin.entrypoint.classloader.group.StaticPluginClassLoaderGroup;
 +import io.papermc.paper.plugin.entrypoint.dependency.GraphDependencyContext;
-+import io.papermc.paper.plugin.entrypoint.dependency.MetaDependencyTree;
++import io.papermc.paper.plugin.entrypoint.dependency.SimpleMetaDependencyTree;
 +import io.papermc.paper.plugin.provider.entrypoint.DependencyContext;
 +import io.papermc.paper.plugin.entrypoint.strategy.modern.ModernPluginLoadingStrategy;
 +import io.papermc.paper.plugin.entrypoint.strategy.ProviderConfiguration;
@@ -397,7 +397,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +                    return false;
 +                }
 +            });
-+            modernPluginLoadingStrategy.loadProviders(pluginProviders, new MetaDependencyTree(GraphBuilder.directed().build()));
++            modernPluginLoadingStrategy.loadProviders(pluginProviders, new SimpleMetaDependencyTree(GraphBuilder.directed().build()));
 +
 +            rootProviders.add(entry.getKey().getDebugName(), entrypoint);
 +        }
@@ -1714,6 +1714,56 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +            '}';
 +    }
 +}
+diff --git a/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/BootstrapMetaDependencyTree.java b/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/BootstrapMetaDependencyTree.java
+new file mode 100644
+index 0000000000000000000000000000000000000000..0000000000000000000000000000000000000000
+--- /dev/null
++++ b/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/BootstrapMetaDependencyTree.java
+@@ -0,0 +0,0 @@
++package io.papermc.paper.plugin.entrypoint.dependency;
++
++import com.google.common.graph.GraphBuilder;
++import com.google.common.graph.MutableGraph;
++import io.papermc.paper.plugin.configuration.PluginMeta;
++import io.papermc.paper.plugin.provider.configuration.PaperPluginMeta;
++
++public class BootstrapMetaDependencyTree extends MetaDependencyTree {
++    public BootstrapMetaDependencyTree() {
++        this(GraphBuilder.directed().build());
++    }
++
++    public BootstrapMetaDependencyTree(MutableGraph<String> graph) {
++        super(graph);
++    }
++
++    @Override
++    protected void registerDependencies(final String identifier, final PluginMeta meta) {
++        if (!(meta instanceof PaperPluginMeta paperPluginMeta)) {
++            throw new IllegalStateException("Only paper plugins can have a bootstrapper!");
++        }
++        // Build a validated provider's dependencies into the graph
++        for (String dependency : paperPluginMeta.getBoostrapDependencies().keySet()) {
++            this.graph.putEdge(identifier, dependency);
++        }
++    }
++
++    @Override
++    protected void unregisterDependencies(final String identifier, final PluginMeta meta) {
++        if (!(meta instanceof PaperPluginMeta paperPluginMeta)) {
++            throw new IllegalStateException("PluginMeta must be a PaperPluginMeta");
++        }
++
++        // Build a validated provider's dependencies into the graph
++        for (String dependency : paperPluginMeta.getBoostrapDependencies().keySet()) {
++            this.graph.removeEdge(identifier, dependency);
++        }
++    }
++
++    @Override
++    public String toString() {
++        return "BootstrapDependencyTree{" + "graph=" + this.graph + '}';
++    }
++}
 diff --git a/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/DependencyContextHolder.java b/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/DependencyContextHolder.java
 new file mode 100644
 index 0000000000000000000000000000000000000000..0000000000000000000000000000000000000000
@@ -1804,17 +1854,16 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +import io.papermc.paper.plugin.provider.PluginProvider;
 +import io.papermc.paper.plugin.provider.entrypoint.DependencyContext;
 +import org.jetbrains.annotations.NotNull;
-+
 +import java.util.HashSet;
 +import java.util.Set;
 +
-+public class MetaDependencyTree implements DependencyContext {
++public abstract class MetaDependencyTree implements DependencyContext {
 +
-+    private final MutableGraph<String> graph;
++    protected final MutableGraph<String> graph;
 +
 +    // We need to upkeep a separate collection since when populating
 +    // a graph it adds nodes even if they are not present
-+    private final Set<String> dependencies = new HashSet<>();
++    protected final Set<String> dependencies = new HashSet<>();
 +
 +    public MetaDependencyTree() {
 +        this(GraphBuilder.directed().build());
@@ -1824,23 +1873,10 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +        this.graph = graph;
 +    }
 +
-+    public void add(PluginProvider<?> provider) {
-+        add(provider.getMeta());
-+    }
-+
-+    public void remove(PluginProvider<?> provider) {
-+        remove(provider.getMeta());
-+    }
-+
 +    public void add(PluginMeta configuration) {
 +        String identifier = configuration.getName();
 +        // Build a validated provider's dependencies into the graph
-+        for (String dependency : configuration.getPluginDependencies()) {
-+            this.graph.putEdge(identifier, dependency);
-+        }
-+        for (String dependency : configuration.getPluginSoftDependencies()) {
-+            this.graph.putEdge(identifier, dependency);
-+        }
++        this.registerDependencies(identifier, configuration);
 +
 +        this.graph.addNode(identifier); // Make sure dependencies at least have a node
 +
@@ -1852,15 +1888,12 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +        this.dependencies.add(identifier);
 +    }
 +
++    protected abstract void registerDependencies(String identifier, PluginMeta meta);
++
 +    public void remove(PluginMeta configuration) {
 +        String identifier = configuration.getName();
 +        // Remove a validated provider's dependencies into the graph
-+        for (String dependency : configuration.getPluginDependencies()) {
-+            this.graph.removeEdge(identifier, dependency);
-+        }
-+        for (String dependency : configuration.getPluginSoftDependencies()) {
-+            this.graph.removeEdge(identifier, dependency);
-+        }
++        this.unregisterDependencies(identifier, configuration);
 +
 +        this.graph.removeNode(identifier); // Remove root node
 +
@@ -1872,6 +1905,8 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +        this.dependencies.remove(identifier);
 +    }
 +
++    protected abstract void unregisterDependencies(String identifier, PluginMeta meta);
++
 +    @Override
 +    public boolean isTransitiveDependency(@NotNull PluginMeta plugin, @NotNull PluginMeta depend) {
 +        String pluginIdentifier = plugin.getName();
@@ -1896,14 +1931,13 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +        return this.dependencies.contains(pluginIdentifier);
 +    }
 +
-+    // Used by the legacy loader -- this isn't recommended
 +    public void addDirectDependency(String dependency) {
 +        this.dependencies.add(dependency);
 +    }
 +
 +    @Override
 +    public String toString() {
-+        return "ProviderDependencyTree{" +
++        return "SimpleDependencyTree{" +
 +            "graph=" + this.graph +
 +            '}';
 +    }
@@ -1911,6 +1945,61 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +    public MutableGraph<String> getGraph() {
 +        return graph;
 +    }
++
++    public void add(PluginProvider<?> provider) {
++        this.add(provider.getMeta());
++    }
++
++    public void remove(PluginProvider<?> provider) {
++        this.remove(provider.getMeta());
++    }
++
++}
+diff --git a/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/SimpleMetaDependencyTree.java b/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/SimpleMetaDependencyTree.java
+new file mode 100644
+index 0000000000000000000000000000000000000000..0000000000000000000000000000000000000000
+--- /dev/null
++++ b/src/main/java/io/papermc/paper/plugin/entrypoint/dependency/SimpleMetaDependencyTree.java
+@@ -0,0 +0,0 @@
++package io.papermc.paper.plugin.entrypoint.dependency;
++
++import com.google.common.graph.GraphBuilder;
++import com.google.common.graph.Graphs;
++import com.google.common.graph.MutableGraph;
++import io.papermc.paper.plugin.configuration.PluginMeta;
++import org.jetbrains.annotations.NotNull;
++
++import java.util.HashSet;
++import java.util.Set;
++
++public class SimpleMetaDependencyTree extends MetaDependencyTree {
++
++    public SimpleMetaDependencyTree() {
++    }
++
++    public SimpleMetaDependencyTree(final MutableGraph<String> graph) {
++        super(graph);
++    }
++
++    @Override
++    protected void registerDependencies(final String identifier, final PluginMeta meta) {
++        for (String dependency : meta.getPluginDependencies()) {
++            this.graph.putEdge(identifier, dependency);
++        }
++        for (String dependency : meta.getPluginSoftDependencies()) {
++            this.graph.putEdge(identifier, dependency);
++        }
++    }
++
++    @Override
++    protected void unregisterDependencies(final String identifier, final PluginMeta meta) {
++        for (String dependency : meta.getPluginDependencies()) {
++            this.graph.removeEdge(identifier, dependency);
++        }
++        for (String dependency : meta.getPluginSoftDependencies()) {
++            this.graph.removeEdge(identifier, dependency);
++        }
++    }
 +}
 diff --git a/src/main/java/io/papermc/paper/plugin/entrypoint/strategy/JohnsonSimpleCycles.java b/src/main/java/io/papermc/paper/plugin/entrypoint/strategy/JohnsonSimpleCycles.java
 new file mode 100644
@@ -3216,7 +3305,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +    }
 +
 +    @Override
-+    public MetaDependencyTree getDependencyTree() {
++    public MetaDependencyTree createDependencyTree() {
 +        return this.dependencyTree;
 +    }
 +}
@@ -3690,6 +3779,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +import io.papermc.paper.plugin.configuration.PluginMeta;
 +import io.papermc.paper.plugin.entrypoint.Entrypoint;
 +import io.papermc.paper.plugin.entrypoint.dependency.MetaDependencyTree;
++import io.papermc.paper.plugin.entrypoint.dependency.SimpleMetaDependencyTree;
 +import io.papermc.paper.plugin.entrypoint.strategy.PluginGraphCycleException;
 +import io.papermc.paper.plugin.provider.classloader.ConfiguredPluginClassLoader;
 +import io.papermc.paper.plugin.provider.classloader.PaperClassLoaderStorage;
@@ -3739,7 +3829,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +    private final CommandMap commandMap;
 +    private final Server server;
 +
-+    private final MetaDependencyTree dependencyTree = new MetaDependencyTree(GraphBuilder.directed().build());
++    private final MetaDependencyTree dependencyTree = new SimpleMetaDependencyTree(GraphBuilder.directed().build());
 +
 +    public PaperPluginInstanceManager(PluginManager pluginManager, CommandMap commandMap, Server server) {
 +        this.commandMap = commandMap;
@@ -4364,7 +4454,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +    }
 +
 +    @Override
-+    public MetaDependencyTree getDependencyTree() {
++    public MetaDependencyTree createDependencyTree() {
 +        return this.dependencyTree;
 +    }
 +}
@@ -6556,7 +6646,9 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +import io.papermc.paper.plugin.bootstrap.BootstrapContext;
 +import io.papermc.paper.plugin.bootstrap.PluginBootstrap;
 +import io.papermc.paper.plugin.bootstrap.PluginBootstrapContextImpl;
++import io.papermc.paper.plugin.entrypoint.dependency.BootstrapMetaDependencyTree;
 +import io.papermc.paper.plugin.entrypoint.dependency.DependencyContextHolder;
++import io.papermc.paper.plugin.entrypoint.dependency.MetaDependencyTree;
 +import io.papermc.paper.plugin.entrypoint.strategy.ProviderConfiguration;
 +import io.papermc.paper.plugin.entrypoint.strategy.modern.ModernPluginLoadingStrategy;
 +import io.papermc.paper.plugin.provider.PluginProvider;
@@ -6603,6 +6695,11 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +    }
 +
 +    @Override
++    public MetaDependencyTree createDependencyTree() {
++        return new BootstrapMetaDependencyTree();
++    }
++
++    @Override
 +    public String toString() {
 +        return "BOOTSTRAP:" + super.toString();
 +    }
@@ -6638,6 +6735,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 @@ -0,0 +0,0 @@
 +package io.papermc.paper.plugin.storage;
 +
++import io.papermc.paper.plugin.entrypoint.dependency.MetaDependencyTree;
 +import io.papermc.paper.plugin.provider.PluginProvider;
 +
 +/**
@@ -6649,6 +6747,8 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +
 +    void register(PluginProvider<T> provider);
 +
++    MetaDependencyTree createDependencyTree();
++
 +    void enter();
 +
 +    Iterable<PluginProvider<T>> getRegisteredProviders();
@@ -6739,10 +6839,9 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +package io.papermc.paper.plugin.storage;
 +
 +import com.google.common.graph.GraphBuilder;
-+import com.google.common.graph.MutableGraph;
 +import com.mojang.logging.LogUtils;
-+import io.papermc.paper.plugin.entrypoint.dependency.GraphDependencyContext;
 +import io.papermc.paper.plugin.entrypoint.dependency.MetaDependencyTree;
++import io.papermc.paper.plugin.entrypoint.dependency.SimpleMetaDependencyTree;
 +import io.papermc.paper.plugin.entrypoint.strategy.PluginGraphCycleException;
 +import io.papermc.paper.plugin.entrypoint.strategy.ProviderLoadingStrategy;
 +import io.papermc.paper.plugin.provider.PluginProvider;
@@ -6774,7 +6873,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +        this.filterLoadingProviders(providerList);
 +
 +        try {
-+            for (ProviderLoadingStrategy.ProviderPair<T> providerPair : this.strategy.loadProviders(providerList, this.getDependencyTree())) {
++            for (ProviderLoadingStrategy.ProviderPair<T> providerPair : this.strategy.loadProviders(providerList, this.createDependencyTree())) {
 +                this.processProvided(providerPair.provider(), providerPair.provided());
 +            }
 +        } catch (PluginGraphCycleException exception) {
@@ -6782,8 +6881,9 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +        }
 +    }
 +
-+    public MetaDependencyTree getDependencyTree() {
-+        return new MetaDependencyTree(GraphBuilder.directed().build());
++    @Override
++    public MetaDependencyTree createDependencyTree() {
++        return new SimpleMetaDependencyTree(GraphBuilder.directed().build());
 +    }
 +
 +    @Override
@@ -7281,6 +7381,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +package io.papermc.paper.plugin;
 +
 +import io.papermc.paper.plugin.entrypoint.dependency.MetaDependencyTree;
++import io.papermc.paper.plugin.entrypoint.dependency.SimpleMetaDependencyTree;
 +import org.junit.jupiter.api.Test;
 +
 +import java.util.List;
@@ -7311,7 +7412,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +
 +    @Test
 +    public void testDependencyTree() {
-+        MetaDependencyTree tree = new MetaDependencyTree();
++        MetaDependencyTree tree = new SimpleMetaDependencyTree();
 +        tree.add(MAIN);
 +        tree.add(HARD_DEPENDENCY_1);
 +        tree.add(SOFT_DEPENDENCY_1);
@@ -7346,7 +7447,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +package io.papermc.paper.plugin;
 +
 +import com.google.common.graph.GraphBuilder;
-+import io.papermc.paper.plugin.entrypoint.dependency.MetaDependencyTree;
++import io.papermc.paper.plugin.entrypoint.dependency.SimpleMetaDependencyTree;
 +import io.papermc.paper.plugin.provider.entrypoint.DependencyContext;
 +import io.papermc.paper.plugin.entrypoint.strategy.modern.ModernPluginLoadingStrategy;
 +import io.papermc.paper.plugin.entrypoint.strategy.ProviderConfiguration;
@@ -7450,7 +7551,7 @@ index 0000000000000000000000000000000000000000..00000000000000000000000000000000
 +
 +        });
 +
-+        modernPluginLoadingStrategy.loadProviders(REGISTERED_PROVIDERS, new MetaDependencyTree(GraphBuilder.directed().build()));
++        modernPluginLoadingStrategy.loadProviders(REGISTERED_PROVIDERS, new SimpleMetaDependencyTree(GraphBuilder.directed().build()));
 +    }
 +
 +    @Test