refactor: Simplify Docker setup and modernize project structure

- Switch from Java to Python scripts (avoids OSGi bundle issues)
- Update pyproject.toml with proper src layout and ruff config
- Add binaries/ and ghidra-src/ to gitignore
- Clean up Module.manifest

.gitignore

@@ -50,3 +50,10 @@ hs_err_pid*
 replay_pid*
 
 /__pycache__
+
+# Docker volumes and binaries
+/binaries/*
+!/binaries/.gitkeep
+
+# Ghidra source (fetched separately)
+/ghidra-src/

docker/Dockerfile

@@ -110,20 +110,16 @@ RUN mkdir -p /opt/ghidra/Ghidra/Extensions \
 RUN mkdir -p /projects /binaries /home/ghidra/.ghidra \
     && chown -R ghidra:ghidra /projects /binaries /home/ghidra
 
-# Copy GhydraMCP scripts to the BSim module's scripts directory
+# Copy GhydraMCP Python scripts to user scripts directory
-# BSim is a working feature module with proper OSGi bundle configuration for scripts
+# Python/Jython scripts don't require OSGi bundle registration - they work without issue
-COPY docker/GhydraMCPServer.java /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/
+RUN mkdir -p /home/ghidra/ghidra_scripts
-COPY docker/ImportRawARM.java /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/
+COPY docker/GhydraMCPServer.py /home/ghidra/ghidra_scripts/
-COPY docker/TestScript.java /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/
+COPY docker/ImportRawARM.java /home/ghidra/ghidra_scripts/
 
-# Set proper ownership, permissions, and timestamp to match Ghidra installation
+# Set proper ownership and permissions
-# Ghidra appears to validate scripts by timestamp - newer files may be rejected
+RUN chown -R ghidra:ghidra /home/ghidra/ghidra_scripts \
-RUN chown ghidra:ghidra /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/GhydraMCPServer.java \
+    && chmod 755 /home/ghidra/ghidra_scripts/*.py 2>/dev/null || true \
-    /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/ImportRawARM.java \
+    && chmod 755 /home/ghidra/ghidra_scripts/*.java 2>/dev/null || true
-    /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/TestScript.java \
-    && touch -t 202508261420 /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/GhydraMCPServer.java \
-    && touch -t 202508261420 /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/ImportRawARM.java \
-    && touch -t 202508261420 /opt/ghidra/Ghidra/Features/BSim/ghidra_scripts/TestScript.java
 
 # Copy entrypoint script (755 so ghidra user can read and execute)
 COPY docker/entrypoint.sh /entrypoint.sh

docker/ImportRawARM.java

@@ -0,0 +1,204 @@
+// Import and analyze raw ARM firmware binary
+// This script imports a raw binary file with specified ARM processor and load address
+// @author GhydraMCP
+// @category Binary.Import
+// @keybinding
+// @menupath
+// @toolbar
+
+import ghidra.app.script.GhidraScript;
+import ghidra.app.util.bin.ByteArrayProvider;
+import ghidra.app.util.importer.MessageLog;
+import ghidra.app.util.opinion.BinaryLoader;
+import ghidra.app.util.opinion.LoadSpec;
+import ghidra.framework.model.DomainFile;
+import ghidra.framework.model.DomainFolder;
+import ghidra.program.model.address.Address;
+import ghidra.program.model.lang.LanguageCompilerSpecPair;
+import ghidra.program.model.listing.Program;
+import ghidra.util.task.TaskMonitor;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.List;
+
+public class ImportRawARM extends GhidraScript {
+
+    @Override
+    public void run() throws Exception {
+        String[] args = getScriptArgs();
+
+        if (args.length < 2) {
+            println("========================================");
+            println("  Import Raw ARM Firmware Binary");
+            println("========================================");
+            println("");
+            println("Usage: -postScript ImportRawARM.java <binary_path> <load_address> [<language_id>]");
+            println("");
+            println("Arguments:");
+            println("  binary_path  - Path to raw binary file");
+            println("  load_address - Base address in hex (e.g., 0x00000000)");
+            println("  language_id  - ARM language ID (default: ARM:LE:32:v5t)");
+            println("");
+            println("Common ARM Language IDs:");
+            println("  ARM:LE:32:v4       - ARMv4 little-endian");
+            println("  ARM:LE:32:v5       - ARMv5 little-endian");
+            println("  ARM:LE:32:v5t      - ARMv5T little-endian (Thumb)");
+            println("  ARM:LE:32:v6       - ARMv6 little-endian");
+            println("  ARM:LE:32:v7       - ARMv7 little-endian");
+            println("  ARM:LE:32:Cortex   - ARM Cortex");
+            println("  ARM:BE:32:v5t      - ARMv5T big-endian");
+            println("");
+            println("Example:");
+            println("  analyzeHeadless /projects MyProject \\");
+            println("    -postScript ImportRawARM.java /binaries/firmware.bin 0x00000000 ARM:LE:32:v5t");
+            println("");
+            return;
+        }
+
+        String binaryPath = args[0];
+        String loadAddressStr = args[1];
+        String languageIDStr = args.length > 2 ? args[2] : "ARM:LE:32:v5t";
+
+        // Parse load address
+        long loadAddress;
+        if (loadAddressStr.toLowerCase().startsWith("0x")) {
+            loadAddress = Long.parseLong(loadAddressStr.substring(2), 16);
+        } else {
+            loadAddress = Long.parseLong(loadAddressStr, 16);
+        }
+
+        File binaryFile = new File(binaryPath);
+        if (!binaryFile.exists()) {
+            printerr("ERROR: Binary file not found: " + binaryPath);
+            return;
+        }
+
+        long fileSize = binaryFile.length();
+
+        println("========================================");
+        println("  Importing Raw ARM Firmware");
+        println("========================================");
+        println("  Binary:       " + binaryFile.getName());
+        println("  Size:         " + fileSize + " bytes (0x" + Long.toHexString(fileSize) + ")");
+        println("  Load Address: 0x" + String.format("%08X", loadAddress));
+        println("  Language:     " + languageIDStr);
+        println("========================================");
+        println("");
+
+        try {
+            // Read the binary file
+            byte[] bytes = Files.readAllBytes(binaryFile.toPath());
+            ByteArrayProvider provider = new ByteArrayProvider(bytes);
+
+            // Parse language string (format: "ARM:LE:32:v5t")
+            String[] parts = languageIDStr.split(":");
+            if (parts.length < 4) {
+                printerr("ERROR: Invalid language ID format. Expected format: ARCH:ENDIAN:SIZE:VARIANT");
+                printerr("       Example: ARM:LE:32:v5t");
+                return;
+            }
+
+            // Create language compiler spec pair
+            LanguageCompilerSpecPair lcsPair = new LanguageCompilerSpecPair(languageIDStr, "default");
+
+            // Use BinaryLoader to import
+            BinaryLoader loader = new BinaryLoader();
+
+            // Create load spec with our language
+            LoadSpec loadSpec = new LoadSpec(loader, loadAddress, lcsPair, false);
+
+            // Get project folder
+            DomainFolder rootFolder = state.getProject().getProjectData().getRootFolder();
+
+            String programName = binaryFile.getName();
+
+            println("Creating program: " + programName);
+            println("Using language: " + languageIDStr);
+            println("");
+
+            // Import using BinaryLoader
+            MessageLog log = new MessageLog();
+            List<Program> programs = loader.load(
+                provider,
+                programName,
+                rootFolder,
+                loadSpec,
+                List.of(),  // options
+                log,
+                this,       // consumer
+                monitor
+            );
+
+            if (programs == null || programs.isEmpty()) {
+                printerr("ERROR: Failed to load binary");
+                println("");
+                println("Loader messages:");
+                println(log.toString());
+                return;
+            }
+
+            Program program = programs.get(0);
+
+            println("Import successful!");
+            println("  Program: " + program.getName());
+            println("  Base Address: " + program.getImageBase());
+            println("  Memory blocks: " + program.getMemory().getBlocks().length);
+            println("");
+
+            // Set entry point at load address
+            Address entryAddr = program.getAddressFactory().getDefaultAddressSpace().getAddress(loadAddress);
+
+            int txId = program.startTransaction("Set Entry Point");
+            try {
+                program.getSymbolTable().addExternalEntryPoint(entryAddr);
+                program.getSymbolTable().createLabel(entryAddr, "entry",
+                    ghidra.program.model.symbol.SourceType.ANALYSIS);
+                program.endTransaction(txId, true);
+
+                println("Entry point set at: " + entryAddr);
+                println("");
+            } catch (Exception e) {
+                program.endTransaction(txId, false);
+                printerr("Warning: Could not set entry point: " + e.getMessage());
+            }
+
+            // Save the program
+            try {
+                program.save("ARM firmware import", monitor);
+                println("Program saved successfully");
+                println("");
+            } catch (Exception e) {
+                printerr("Warning: Could not save program: " + e.getMessage());
+            }
+
+            // Run analysis
+            println("Starting auto-analysis...");
+            println("(This may take a while for large binaries)");
+            println("");
+
+            analyzeAll(program);
+
+            println("");
+            println("========================================");
+            println("  Import Complete!");
+            println("========================================");
+            println("  Program: " + program.getName());
+            println("  Functions found: " + program.getFunctionManager().getFunctionCount());
+            println("  Defined data: " + program.getListing().getNumDefinedData());
+            println("========================================");
+            println("");
+
+            // Set as current program for subsequent scripts
+            state.setCurrentProgram(program);
+
+        } catch (IOException e) {
+            printerr("ERROR: Failed to read binary file: " + e.getMessage());
+            e.printStackTrace();
+        } catch (Exception e) {
+            printerr("ERROR: Import failed: " + e.getMessage());
+            e.printStackTrace();
+        }
+    }
+}

pyproject.toml

@@ -1,21 +1,42 @@
 [project]
 name = "ghydramcp"
-version = "2025.12.1"
+version = "2025.12.3"
 description = "AI-assisted reverse engineering bridge: a multi-instance Ghidra plugin exposed via a HATEOAS REST API plus an MCP Python bridge for decompilation, analysis & binary manipulation"
 readme = "README.md"
 requires-python = ">=3.11"
+authors = [
+    {name = "Ryan Malloy", email = "ryan@supported.systems"}
+]
 dependencies = [
     "mcp>=1.22.0",
     "requests>=2.32.3",
+    "fastmcp>=2.0.0",
 ]
 
 [project.scripts]
-ghydramcp = "bridge_mcp_hydra:main"
+ghydramcp = "ghydramcp:main"
 
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
-packages = ["."]
+packages = ["src/ghydramcp"]
-only-include = ["bridge_mcp_hydra.py"]
+
+[tool.hatch.build]
+sources = ["src"]
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/src",
+    "/README.md",
+    "/pyproject.toml",
+]
+
+[tool.ruff]
+line-length = 100
+target-version = "py311"
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "W"]
+ignore = ["E501"]  # Line too long - handled by formatter

src/main/resources/Module.manifest

@@ -1,3 +1,9 @@
-Manifest-Version: 1.0
+# GhydraMCP Module Manifest
-GHIDRA_MODULE_NAME: GhydraMCP
+#
-GHIDRA_MODULE_DESC: A multi-headed REST interface for Ghidra for use with MCP agents.
+# This file lists third-party libraries bundled with this extension and their licenses.
+# Module metadata (name, description, version) is defined in extension.properties.
+#
+# Format: MODULE FILE LICENSE: lib/filename.jar License Name
+#
+# Currently, GhydraMCP has no bundled third-party libraries.
+# Gson is provided by Ghidra itself.