Rework MCP server

app/src/main/java/io/xpipe/app/beacon/mcp/AppMcpServer.java

@@ -46,6 +46,11 @@ public class AppMcpServer {
                 (serverRequest) -> McpTransportContext.EMPTY,
                 null);
 
+        var prompt = McpSchemaFiles.load("prompt.md");
+        var effectivePrompt = AppPrefs.get().mcpAdditionalContext().getValue() != null ?
+                prompt.replace("__CUSTOM__", AppPrefs.get().mcpAdditionalContext().getValue()) :
+                prompt.replace("__CUSTOM__", "");
+
         McpSyncServer syncServer = io.modelcontextprotocol.server.McpServer.sync(transportProvider)
                 .serverInfo(AppNames.ofCurrent().getName(), AppProperties.get().getVersion())
                 .capabilities(McpSchema.ServerCapabilities.builder()
@@ -53,7 +58,7 @@ public class AppMcpServer {
                         .tools(true)
                         .prompts(false)
                         .build())
-                .instructions(AppPrefs.get().mcpAdditionalContext().getValue())
+                .instructions(effectivePrompt)
                 .build();
 
         var readOnlyTools = new ArrayList<McpServerFeatures.SyncToolSpecification>();
@@ -66,7 +71,6 @@ public class AppMcpServer {
 
         var mutationTools = new ArrayList<McpServerFeatures.SyncToolSpecification>();
         mutationTools.add(McpTools.openTerminal());
-        mutationTools.add(McpTools.openTerminalInline());
         mutationTools.add(McpTools.createFile());
         mutationTools.add(McpTools.writeFile());
         mutationTools.add(McpTools.createDirectory());

app/src/main/java/io/xpipe/app/beacon/mcp/McpToolHandler.java

@@ -2,6 +2,7 @@ package io.xpipe.app.beacon.mcp;
 
 import io.xpipe.app.ext.ShellStore;
 import io.xpipe.app.issue.ErrorEventFactory;
+import io.xpipe.app.process.ShellControl;
 import io.xpipe.app.storage.DataStorage;
 import io.xpipe.app.storage.DataStorageQuery;
 import io.xpipe.app.storage.DataStoreEntry;
@@ -113,13 +114,13 @@ public interface McpToolHandler
             return b;
         }
 
-        public FilePath getFilePath(String key) throws BeaconClientException {
+        public FilePath getFilePath(ShellControl sc, String key) throws Exception {
             var s = getStringArgument(key);
             var path = FilePath.parse(s);
             if (path == null) {
                 throw new BeaconClientException("Invalid argument for key " + key);
             }
-            return path;
+            return path.resolveTildeHome(sc.view().userHome());
         }
 
         public DataStoreEntryRef<?> getDataStoreRef(String name) throws BeaconClientException {
@@ -130,7 +131,7 @@ public interface McpToolHandler
 
             if (found.size() > 1) {
                 throw new BeaconClientException("Multiple connections found: "
-                        + found.stream().map(DataStoreEntry::getName).toList());
+                        + found.stream().map(entry -> DataStorage.get().getStorePath(entry).toString()).toList());
             }
 
             var e = found.getFirst();

app/src/main/java/io/xpipe/app/beacon/mcp/McpTools.java

@@ -63,6 +63,9 @@ public final class McpTools {
                                             + syncToolSpecification.tool().description())
                             .collect(Collectors.joining("\n"));
 
+                    var muEnabled = AppPrefs.get().enableMcpMutationTools().get();
+                    var muStatus = muEnabled ? "Right now, the mutation tools are enabled." : "Right now, the mutation tools are disabled. When you enable them in the settings menu, the MCP client might need a reconnect to see the changes.";
+
                     var text = """
                                The XPipe MCP server offers the following read-only tools:
                                %s
@@ -71,7 +74,8 @@ public final class McpTools {
                                You can also enable the following potentially destructive tools in the settings menu:
                                %s
                                These tools can perform write operations and other actions that might be potentially destructive.
-                               """.formatted(roList, muList);
+                               %s
+                               """.formatted(roList, muList, muStatus);
 
                     return McpSchema.CallToolResult.builder()
                             .addTextContent(text)
@@ -138,10 +142,8 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var filter = req.getOptionalStringArgument("filter");
-                    var entries = filter.isPresent()
-                            ? DataStorageQuery.queryUserInput(filter.get())
-                            : DataStorage.get().getStoreEntries();
+                    var filter = req.getStringArgument("filter");
+                    var entries = DataStorageQuery.queryUserInput(filter);
 
                     var list = new ArrayList<ConnectionResource>();
                     for (var e : entries) {
@@ -192,10 +194,10 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var path = req.getFilePath("path");
                     var system = req.getStringArgument("system");
                     var shellStore = req.getShellStoreRef(system, false);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
+                    var path = req.getFilePath(shellSession.getControl(), "path");
                     var fs = new ConnectionFileSystem(shellSession.getControl());
 
                     if (!fs.fileExists(path)) {
@@ -218,12 +220,12 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var path = req.getFilePath("path");
                     var system = req.getStringArgument("system");
                     var recursive = req.getOptionalBooleanArgument("recursive").orElse(false);
                     var shellStore = req.getShellStoreRef(system, false);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
                     var fs = new ConnectionFileSystem(shellSession.getControl());
+                    var path = req.getFilePath(shellSession.getControl(), "path");
 
                     if (!fs.directoryExists(path)) {
                         throw new BeaconClientException("Directory " + path + " does not exist");
@@ -246,12 +248,11 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var path = req.getFilePath("path");
                     var system = req.getStringArgument("system");
-                    var recursive = req.getOptionalBooleanArgument("recursive").orElse(false);
                     var pattern = req.getStringArgument("name");
                     var shellStore = req.getShellStoreRef(system, false);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
+                    var path = req.getFilePath(shellSession.getControl(), "path");
                     var fs = new ConnectionFileSystem(shellSession.getControl());
 
                     if (!fs.directoryExists(path)) {
@@ -259,7 +260,7 @@ public final class McpTools {
                     }
 
                     var regex = Pattern.compile(DataStorageQuery.toRegex(pattern));
-                    try (var stream = recursive ? fs.listFilesRecursively(fs, path).stream() : fs.listFiles(fs, path)) {
+                    try (var stream = fs.listFiles(fs, path)) {
                         var list = stream.toList();
                         var builder = McpSchema.CallToolResult.builder();
                         list.stream()
@@ -280,10 +281,10 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var path = req.getFilePath("path");
                     var system = req.getStringArgument("system");
                     var shellStore = req.getShellStoreRef(system, false);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
+                    var path = req.getFilePath(shellSession.getControl(), "path");
                     var fs = new ConnectionFileSystem(shellSession.getControl());
 
                     if (!fs.fileExists(path) && !fs.directoryExists(path)) {
@@ -321,10 +322,10 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var path = req.getFilePath("path");
                     var system = req.getStringArgument("system");
                     var shellStore = req.getShellStoreRef(system, true);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
+                    var path = req.getFilePath(shellSession.getControl(), "path");
                     var fs = new ConnectionFileSystem(shellSession.getControl());
 
                     if (fs.fileExists(path)) {
@@ -353,11 +354,11 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var path = req.getFilePath("path");
                     var system = req.getStringArgument("system");
                     var content = req.getStringArgument("content");
                     var shellStore = req.getShellStoreRef(system, true);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
+                    var path = req.getFilePath(shellSession.getControl(), "path");
                     var fs = new ConnectionFileSystem(shellSession.getControl());
 
                     var b = content.getBytes(StandardCharsets.UTF_8);
@@ -377,10 +378,10 @@ public final class McpTools {
         return McpServerFeatures.SyncToolSpecification.builder()
                 .tool(tool)
                 .callHandler(McpToolHandler.of((req) -> {
-                    var path = req.getFilePath("path");
                     var system = req.getStringArgument("system");
                     var shellStore = req.getShellStoreRef(system, true);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
+                    var path = req.getFilePath(shellSession.getControl(), "path");
                     var fs = new ConnectionFileSystem(shellSession.getControl());
 
                     if (fs.fileExists(path)) {
@@ -406,12 +407,8 @@ public final class McpTools {
                     var shellStore = req.getShellStoreRef(system, true);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
 
-                    var out = ProcessControlProvider.get().executeMcpCommand(shellSession.getControl(), command);
-                    var formatted = CommandDialog.formatOutput(out);
-
-                    return McpSchema.CallToolResult.builder()
-                            .addTextContent(formatted)
-                            .build();
+                    var r = ProcessControlProvider.get().executeMcpCommand(shellSession.getControl(), command);
+                    return r;
                 }))
                 .build();
     }
@@ -423,11 +420,11 @@ public final class McpTools {
                 .callHandler(McpToolHandler.of((req) -> {
                     var system = req.getStringArgument("system");
                     var script = req.getDataStoreRef("script");
-                    var directory = req.getFilePath("directory");
                     var arguments = req.getStringArgument("arguments");
 
                     var shellStore = req.getShellStoreRef(system, true);
                     var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
+                    var directory = req.getFilePath(shellSession.getControl(), "directory");
 
                     var clazz = Class.forName(
                             AppExtensionManager.getInstance()
@@ -479,34 +476,6 @@ public final class McpTools {
                 .build();
     }
 
-    public static McpServerFeatures.SyncToolSpecification openTerminalInline() throws IOException {
-        var tool = McpSchemaFiles.loadTool("open_terminal_inline.json");
-        return McpServerFeatures.SyncToolSpecification.builder()
-                .tool(tool)
-                .callHandler(McpToolHandler.of((req) -> {
-                    var system = req.getStringArgument("system");
-                    var directory = req.getOptionalStringArgument("directory");
-                    var shellStore = req.getShellStoreRef(system, true);
-                    var shellSession = AppBeaconServer.get().getCache().getOrStart(shellStore);
-
-                    var script = shellSession
-                            .getControl()
-                            .prepareTerminalOpen(
-                                    TerminalInitScriptConfig.ofName(
-                                            shellStore.get().getName()),
-                                    directory.isPresent()
-                                            ? WorkingDirectoryFunction.fixed(FilePath.parse(directory.get()))
-                                            : WorkingDirectoryFunction.none());
-
-                    var json = JsonNodeFactory.instance.objectNode();
-                    json.put("command", script);
-                    return McpSchema.CallToolResult.builder()
-                            .structuredContent(JacksonMapper.getDefault().writeValueAsString(json))
-                            .build();
-                }))
-                .build();
-    }
-
     public static McpServerFeatures.SyncToolSpecification toggleState() throws IOException {
         var tool = McpSchemaFiles.loadTool("toggle_state.json");
         return McpServerFeatures.SyncToolSpecification.builder()

app/src/main/java/io/xpipe/app/ext/ProcessControlProvider.java

@@ -1,5 +1,6 @@
 package io.xpipe.app.ext;
 
+import io.modelcontextprotocol.spec.McpSchema;
 import io.xpipe.app.browser.BrowserFullSessionModel;
 import io.xpipe.app.browser.BrowserStoreSessionTab;
 import io.xpipe.app.comp.base.ModalOverlay;
@@ -58,7 +59,7 @@ public abstract class ProcessControlProvider {
 
     public abstract ShellDialect getEffectiveLocalDialect();
 
-    public abstract String executeMcpCommand(ShellControl sc, String command) throws Exception;
+    public abstract McpSchema.CallToolResult executeMcpCommand(ShellControl sc, String command) throws Exception;
 
     public ShellDialect getNextFallbackDialect() {
         var av = getAvailableLocalDialects();

app/src/main/java/io/xpipe/app/secret/SecretQueryState.java

@@ -20,7 +20,7 @@ public enum SecretQueryState {
                 yield "Authentication operation was cancelled";
             }
             case NON_INTERACTIVE -> {
-                yield "Session is not interactive but required user input for authentication";
+                yield "Session is not interactive but required user input for authentication as no password is preconfigured";
             }
             case FIXED_SECRET_WRONG -> {
                 yield "Authentication failed: Provided authentication secret was not accepted by the server, probably because it is incorrect";