Add security hardening, Ghidra, recreate skill, checkpoints, shells, web search and themes

- Sandbox (bubblewrap) for non-admin shell/git, MCP per-user rights, hard budgets and quotas,
  login rate limiting, audit log and backups
- Ghidra headless decompilation (ARM64 natives built from source), binary_info tool,
  clean room / deep workflow per session
- Recreate skill and commands for analysing and re-building old software
- File checkpoints with rewind/restore, background shells (bash_output, kill_shell)
- web_search tool (DuckDuckGo, SearXNG, Brave, Tavily)
- In-app dialogs and toasts instead of browser dialogs
- 15 base themes (trilium-themes palettes plus Nord, VS Code, GitHub, Catppuccin, One,
  Dracula, Rose Pine, Everforest, Kanagawa) with light/dark/auto switcher and license notes

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

server/ghidra/CodeCraftExport.java

@@ -0,0 +1,111 @@
+// Exports a Ghidra analysis for CodeCraft: program info, function index,
+// pseudo-C per function, strings, imports and exports.
+// Usage: analyzeHeadless ... -postScript CodeCraftExport.java <output dir> [max functions]
+//@category CodeCraft
+
+import ghidra.app.decompiler.DecompInterface;
+import ghidra.app.decompiler.DecompileResults;
+import ghidra.app.script.GhidraScript;
+import ghidra.program.model.address.Address;
+import ghidra.program.model.address.AddressIterator;
+import ghidra.program.model.listing.Data;
+import ghidra.program.model.listing.Function;
+import ghidra.program.model.listing.FunctionIterator;
+import ghidra.program.model.listing.Program;
+import ghidra.program.model.symbol.Symbol;
+import ghidra.program.model.symbol.SymbolIterator;
+import ghidra.program.util.DefinedStringIterator;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+
+public class CodeCraftExport extends GhidraScript {
+
+    private static String clean(String s) {
+        return s.replace("\\", "\\\\").replace("\n", "\\n").replace("\r", "\\r").replace("\t", "\\t");
+    }
+
+    @Override
+    public void run() throws Exception {
+        String[] args = getScriptArgs();
+        File out = new File(args[0]);
+        int maxFunctions = args.length > 1 ? Integer.parseInt(args[1]) : Integer.MAX_VALUE;
+        File funcDir = new File(out, "functions");
+        funcDir.mkdirs();
+        Program p = currentProgram;
+
+        try (PrintWriter info = new PrintWriter(new File(out, "info.txt"), StandardCharsets.UTF_8)) {
+            info.println("name: " + p.getName());
+            info.println("format: " + p.getExecutableFormat());
+            info.println("language: " + p.getLanguageID());
+            info.println("compiler: " + p.getCompilerSpec().getCompilerSpecID());
+            info.println("image_base: " + p.getImageBase());
+            info.println("functions: " + p.getFunctionManager().getFunctionCount());
+        }
+
+        DecompInterface di = new DecompInterface();
+        di.openProgram(p);
+        int n = 0;
+        try (PrintWriter idx = new PrintWriter(new File(out, "functions.tsv"), StandardCharsets.UTF_8)) {
+            idx.println("address\tname\tsize\tfile\tsignature");
+            FunctionIterator it = p.getFunctionManager().getFunctions(true);
+            while (it.hasNext() && !monitor.isCancelled() && n < maxFunctions) {
+                Function f = it.next();
+                if (f.isThunk() || f.isExternal()) {
+                    continue;
+                }
+                String base = f.getEntryPoint().toString() + "_" + f.getName().replaceAll("[^A-Za-z0-9_]", "_");
+                if (base.length() > 120) {
+                    base = base.substring(0, 120);
+                }
+                DecompileResults r = di.decompileFunction(f, 60, monitor);
+                String code = (r != null && r.decompileCompleted())
+                        ? r.getDecompiledFunction().getC()
+                        : "/* decompilation failed: " + (r == null ? "no result" : r.getErrorMessage()) + " */\n";
+                Files.writeString(new File(funcDir, base + ".c").toPath(),
+                        "// " + f.getName() + " @ " + f.getEntryPoint() + "\n" + code, StandardCharsets.UTF_8);
+                idx.println(f.getEntryPoint() + "\t" + f.getName() + "\t" + f.getBody().getNumAddresses()
+                        + "\tfunctions/" + base + ".c\t" + clean(f.getSignature().getPrototypeString()));
+                n++;
+                if (n % 200 == 0) {
+                    println("CodeCraft: decompiled " + n + " functions");
+                }
+            }
+        }
+        di.dispose();
+
+        try (PrintWriter sw = new PrintWriter(new File(out, "strings.tsv"), StandardCharsets.UTF_8)) {
+            sw.println("address\tstring");
+            for (Data d : DefinedStringIterator.forProgram(p)) {
+                Object v = d.getValue();
+                if (v != null) {
+                    sw.println(d.getAddress() + "\t" + clean(v.toString()));
+                }
+            }
+        }
+
+        try (PrintWriter iw = new PrintWriter(new File(out, "imports.tsv"), StandardCharsets.UTF_8)) {
+            iw.println("library\tname");
+            SymbolIterator si = p.getSymbolTable().getExternalSymbols();
+            while (si.hasNext()) {
+                Symbol s = si.next();
+                iw.println(s.getParentNamespace().getName() + "\t" + s.getName());
+            }
+        }
+
+        try (PrintWriter ew = new PrintWriter(new File(out, "exports.tsv"), StandardCharsets.UTF_8)) {
+            ew.println("name\taddress");
+            AddressIterator ai = p.getSymbolTable().getExternalEntryPointIterator();
+            while (ai.hasNext()) {
+                Address a = ai.next();
+                Symbol s = p.getSymbolTable().getPrimarySymbol(a);
+                ew.println((s == null ? "?" : s.getName()) + "\t" + a);
+            }
+        }
+
+        Files.writeString(new File(out, ".done").toPath(), String.valueOf(n), StandardCharsets.UTF_8);
+        println("CodeCraft: export complete, " + n + " functions");
+    }
+}