Removed invasive brandingHEADmaster

1 files changed, 1024 insertions, 0 deletions

diff --git a/src/com/pkrandom/ctr/NCCH.java b/src/com/pkrandom/ctr/NCCH.java
new file mode 100644
index 0000000..9a326a5
--- /dev/null
+++ b/src/com/pkrandom/ctr/NCCH.java
@@ -0,0 +1,1024 @@
+package com.pkrandom.ctr;
+
+/*----------------------------------------------------------------------------*/
+/*--  NCCH.java - a base class for dealing with 3DS NCCH ROM images.        --*/
+/*--                                                                        --*/
+/*--  Part of "Universal Pokemon Randomizer ZX" by the UPR-ZX team          --*/
+/*--  Pokemon and any associated names and the like are                     --*/
+/*--  trademark and (C) Nintendo 1996-2020.                                 --*/
+/*--                                                                        --*/
+/*--  This program is free software: you can redistribute it and/or modify  --*/
+/*--  it under the terms of the GNU General Public License as published by  --*/
+/*--  the Free Software Foundation, either version 3 of the License, or     --*/
+/*--  (at your option) any later version.                                   --*/
+/*--                                                                        --*/
+/*--  This program is distributed in the hope that it will be useful,       --*/
+/*--  but WITHOUT ANY WARRANTY; without even the implied warranty of        --*/
+/*--  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the          --*/
+/*--  GNU General Public License for more details.                          --*/
+/*--                                                                        --*/
+/*--  You should have received a copy of the GNU General Public License     --*/
+/*--  along with this program. If not, see <http://www.gnu.org/licenses/>.  --*/
+/*----------------------------------------------------------------------------*/
+
+import com.pkrandom.FileFunctions;
+import com.pkrandom.SysConstants;
+import com.pkrandom.exceptions.CannotWriteToLocationException;
+import com.pkrandom.exceptions.EncryptedROMException;
+import com.pkrandom.exceptions.RandomizerIOException;
+import cuecompressors.BLZCoder;
+
+import java.io.*;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.security.*;
+import java.util.*;
+
+public class NCCH {
+    private String romFilename;
+    private RandomAccessFile baseRom;
+    private long ncchStartingOffset;
+    private String productCode;
+    private String titleId;
+    private int version;
+    private long exefsOffset, romfsOffset, fileDataOffset;
+    private ExefsFileHeader codeFileHeader;
+    private SMDH smdh;
+    private List<ExefsFileHeader> extraExefsFiles;
+    private List<FileMetadata> fileMetadataList;
+    private Map<String, RomfsFile> romfsFiles;
+    private boolean romOpen;
+    private String tmpFolder;
+    private boolean writingEnabled;
+    private boolean codeCompressed, codeOpen, codeChanged;
+    private byte[] codeRamstored;
+
+    // Public so the base game can read it from the game update NCCH
+    public long originalCodeCRC, originalRomfsHeaderCRC;
+
+    private static final int media_unit_size = 0x200;
+    private static final int header_and_exheader_size = 0xA00;
+    private static final int ncsd_magic = 0x4E435344;
+    private static final int cia_header_size = 0x2020;
+    private static final int ncch_magic = 0x4E434348;
+    private static final int ncch_and_ncsd_magic_offset = 0x100;
+    private static final int exefs_header_size = 0x200;
+    private static final int romfs_header_size = 0x5C;
+    private static final int romfs_magic_1 = 0x49564643;
+    private static final int romfs_magic_2 = 0x00000100;
+    private static final int level3_header_size = 0x28;
+    private static final int metadata_unused = 0xFFFFFFFF;
+
+    public NCCH(String filename, String productCode, String titleId) throws IOException {
+        this.romFilename = filename;
+        this.baseRom = new RandomAccessFile(filename, "r");
+        this.ncchStartingOffset = NCCH.getCXIOffsetInFile(filename);
+        this.productCode = productCode;
+        this.titleId = titleId;
+        this.romOpen = true;
+
+        if (this.ncchStartingOffset != -1) {
+            this.version = this.readVersionFromFile();
+        }
+
+        // TMP folder?
+        String rawFilename = new File(filename).getName();
+        String dataFolder = "tmp_" + rawFilename.substring(0, rawFilename.lastIndexOf('.'));
+        // remove nonsensical chars
+        dataFolder = dataFolder.replaceAll("[^A-Za-z0-9_]+", "");
+        File tmpFolder = new File(SysConstants.ROOT_PATH + dataFolder);
+        tmpFolder.mkdirs();
+        if (tmpFolder.canWrite()) {
+            writingEnabled = true;
+            this.tmpFolder = SysConstants.ROOT_PATH + dataFolder + File.separator;
+            tmpFolder.deleteOnExit();
+        } else {
+            writingEnabled = false;
+        }
+
+        // The below code handles things "wrong" with regards to encrypted ROMs. We just
+        // blindly treat the ROM as decrypted and try to parse all of its data, when we
+        // *should* be looking at the header of the ROM to determine if the ROM is encrypted.
+        // Unfortunately, many people have poorly-decrypted ROMs that do not properly set
+        // the bytes on the NCCH header, so we can't assume that the header is telling the
+        // truth. If we read the whole ROM without crashing, then it's probably decrypted.
+        try {
+            readFileSystem();
+        } catch (Exception ex) {
+            if (!this.isDecrypted()) {
+                throw new EncryptedROMException(ex);
+            } else {
+                throw ex;
+            }
+        }
+    }
+
+    public void reopenROM() throws IOException {
+        if (!this.romOpen) {
+            baseRom = new RandomAccessFile(this.romFilename, "r");
+            romOpen = true;
+        }
+    }
+
+    public void closeROM() throws IOException {
+        if (this.romOpen && baseRom != null) {
+            baseRom.close();
+            baseRom = null;
+            romOpen = false;
+        }
+    }
+
+    private void readFileSystem() throws IOException {
+        exefsOffset = ncchStartingOffset + FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x1A0) * media_unit_size;
+        romfsOffset = ncchStartingOffset + FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x1B0) * media_unit_size;
+        baseRom.seek(ncchStartingOffset + 0x20D);
+        byte systemControlInfoFlags = baseRom.readByte();
+        codeCompressed = (systemControlInfoFlags & 0x01) != 0;
+        readExefs();
+        readRomfs();
+    }
+
+    private void readExefs() throws IOException {
+        System.out.println("NCCH: Reading exefs...");
+        byte[] exefsHeaderData = new byte[exefs_header_size];
+        baseRom.seek(exefsOffset);
+        baseRom.readFully(exefsHeaderData);
+
+        ExefsFileHeader[] fileHeaders = new ExefsFileHeader[10];
+        for (int i = 0; i < 10; i++) {
+            fileHeaders[i] = new ExefsFileHeader(exefsHeaderData, i * 0x10);
+        }
+
+        extraExefsFiles = new ArrayList<>();
+        for (ExefsFileHeader fileHeader : fileHeaders) {
+            if (fileHeader.isValid() && fileHeader.filename.equals(".code")) {
+                codeFileHeader = fileHeader;
+            } else if (fileHeader.isValid()) {
+                extraExefsFiles.add(fileHeader);
+            }
+
+            if (fileHeader.isValid() && fileHeader.filename.equals("icon")) {
+                byte[] smdhBytes = new byte[fileHeader.size];
+                baseRom.seek(exefsOffset + 0x200 + fileHeader.offset);
+                baseRom.readFully(smdhBytes);
+                smdh = new SMDH(smdhBytes);
+            }
+        }
+        System.out.println("NCCH: Done reading exefs");
+    }
+
+    private void readRomfs() throws IOException {
+        System.out.println("NCCH: Reading romfs...");
+        byte[] romfsHeaderData = new byte[romfs_header_size];
+        baseRom.seek(romfsOffset);
+        baseRom.readFully(romfsHeaderData);
+        originalRomfsHeaderCRC = FileFunctions.getCRC32(romfsHeaderData);
+        int magic1 = FileFunctions.readFullIntBigEndian(romfsHeaderData, 0x00);
+        int magic2 = FileFunctions.readFullIntBigEndian(romfsHeaderData, 0x04);
+        if (magic1 != romfs_magic_1 || magic2 != romfs_magic_2) {
+            System.err.println("NCCH: romfs does not contain magic values");
+            // Not a valid romfs
+            return;
+        }
+        int masterHashSize = FileFunctions.readFullInt(romfsHeaderData, 0x08);
+        int level3HashBlockSize = 1 << FileFunctions.readFullInt(romfsHeaderData, 0x4C);
+        long level3Offset = romfsOffset + alignLong(0x60 + masterHashSize, level3HashBlockSize);
+
+        byte[] level3HeaderData = new byte[level3_header_size];
+        baseRom.seek(level3Offset);
+        baseRom.readFully(level3HeaderData);
+        int headerLength = FileFunctions.readFullInt(level3HeaderData, 0x00);
+        if (headerLength != level3_header_size) {
+            // Not a valid romfs
+            System.err.println("NCCH: romfs does not have a proper level 3 header");
+            return;
+        }
+        int directoryMetadataOffset = FileFunctions.readFullInt(level3HeaderData, 0x0C);
+        int directoryMetadataLength = FileFunctions.readFullInt(level3HeaderData, 0x10);
+        int fileMetadataOffset = FileFunctions.readFullInt(level3HeaderData, 0x1c);
+        int fileMetadataLength = FileFunctions.readFullInt(level3HeaderData, 0x20);
+        int fileDataOffsetFromHeaderStart = FileFunctions.readFullInt(level3HeaderData, 0x24);
+        fileDataOffset = level3Offset + fileDataOffsetFromHeaderStart;
+
+        byte[] directoryMetadataBlock = new byte[directoryMetadataLength];
+        baseRom.seek(level3Offset + directoryMetadataOffset);
+        baseRom.readFully(directoryMetadataBlock);
+        byte[] fileMetadataBlock = new byte[fileMetadataLength];
+        baseRom.seek(level3Offset + fileMetadataOffset);
+        baseRom.readFully(fileMetadataBlock);
+        fileMetadataList = new ArrayList<>();
+        romfsFiles = new TreeMap<>();
+        visitDirectory(0, "", directoryMetadataBlock, fileMetadataBlock);
+        System.out.println("NCCH: Done reading romfs");
+    }
+
+    private void visitDirectory(int offset, String rootPath, byte[] directoryMetadataBlock, byte[] fileMetadataBlock) {
+        DirectoryMetadata metadata = new DirectoryMetadata(directoryMetadataBlock, offset);
+        String currentPath = rootPath;
+        if (!metadata.name.equals("")) {
+            currentPath = rootPath + metadata.name + "/";
+        }
+
+        if (metadata.firstFileOffset != metadata_unused) {
+            visitFile(metadata.firstFileOffset, currentPath, fileMetadataBlock);
+        }
+        if (metadata.firstChildDirectoryOffset != metadata_unused) {
+            visitDirectory(metadata.firstChildDirectoryOffset, currentPath, directoryMetadataBlock, fileMetadataBlock);
+        }
+        if (metadata.siblingDirectoryOffset != metadata_unused) {
+            visitDirectory(metadata.siblingDirectoryOffset, rootPath, directoryMetadataBlock, fileMetadataBlock);
+        }
+    }
+
+    private void visitFile(int offset, String rootPath, byte[] fileMetadataBlock) {
+        FileMetadata metadata = new FileMetadata(fileMetadataBlock, offset);
+        String currentPath = rootPath + metadata.name;
+        System.out.println("NCCH: Visiting file " + currentPath);
+        RomfsFile file = new RomfsFile(this);
+        file.offset = fileDataOffset + metadata.fileDataOffset;
+        file.size = (int) metadata.fileDataLength;  // no Pokemon game has a file larger than unsigned int max
+        file.fullPath = currentPath;
+        metadata.file = file;
+        fileMetadataList.add(metadata);
+        romfsFiles.put(currentPath, file);
+        if (metadata.siblingFileOffset != metadata_unused) {
+            visitFile(metadata.siblingFileOffset, rootPath, fileMetadataBlock);
+        }
+    }
+
+    public void saveAsNCCH(String filename, String gameAcronym, long seed) throws IOException, NoSuchAlgorithmException {
+        this.reopenROM();
+
+        // Initialize new ROM
+        RandomAccessFile fNew = new RandomAccessFile(filename, "rw");
+
+        // Read the header and exheader and write it to the output ROM
+        byte[] header = new byte[header_and_exheader_size];
+        baseRom.seek(ncchStartingOffset);
+        baseRom.readFully(header);
+        fNew.write(header);
+
+        // Just in case they were set wrong in the original header, let's correctly set the
+        // bytes in the header to indicate the output ROM is decrypted
+        byte[] flags = new byte[8];
+        baseRom.seek(ncchStartingOffset + 0x188);
+        baseRom.readFully(flags);
+        flags[3] = 0;
+        flags[7] = 4;
+        fNew.seek(0x188);
+        fNew.write(flags);
+
+        // The logo is small enough (8KB) to just read the whole thing into memory. Write it to the new ROM directly
+        // after the header, then update the new ROM's logo offset
+        long logoOffset = ncchStartingOffset + FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x198) * media_unit_size;
+        long logoLength = FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x19C) * media_unit_size;
+        if (logoLength > 0) {
+            byte[] logo = new byte[(int) logoLength];
+            baseRom.seek(logoOffset);
+            baseRom.readFully(logo);
+            long newLogoOffset = header_and_exheader_size;
+            fNew.seek(newLogoOffset);
+            fNew.write(logo);
+            fNew.seek(0x198);
+            fNew.write((int) newLogoOffset / media_unit_size);
+        }
+
+        // The plain region is even smaller (1KB) so repeat the same process
+        long plainOffset = ncchStartingOffset + FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x190) * media_unit_size;
+        long plainLength = FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x194) * media_unit_size;
+        if (plainLength > 0) {
+            byte[] plain = new byte[(int) plainLength];
+            baseRom.seek(plainOffset);
+            baseRom.readFully(plain);
+            long newPlainOffset = header_and_exheader_size + logoLength;
+            fNew.seek(newPlainOffset);
+            fNew.write(plain);
+            fNew.seek(0x190);
+            fNew.write((int) newPlainOffset / media_unit_size);
+        }
+
+        // Update the SMDH so that Citra displays the seed in the title
+        smdh.setAllDescriptions(gameAcronym + " randomizer seed: " + seed);
+        smdh.setAllPublishers("Universal Pokemon Randomizer ZX");
+
+        // Now, reconstruct the exefs based on our new version of .code and our new SMDH
+        long newExefsOffset = header_and_exheader_size + logoLength + plainLength;
+        long newExefsLength = rebuildExefs(fNew, newExefsOffset);
+        fNew.seek(0x1A0);
+        fNew.write((int) newExefsOffset / media_unit_size);
+        fNew.seek(0x1A4);
+        fNew.write((int) newExefsLength / media_unit_size);
+
+        // Then, reconstruct the romfs
+        // TODO: Fix the yet-unsolved alignment issues in rebuildRomfs when you remove this align
+        long newRomfsOffset = alignLong(header_and_exheader_size + logoLength + plainLength + newExefsLength, 4096);
+        long newRomfsLength = rebuildRomfs(fNew, newRomfsOffset);
+        fNew.seek(0x1B0);
+        fNew.write((int) newRomfsOffset / media_unit_size);
+        fNew.seek(0x1B4);
+        fNew.write((int) newRomfsLength / media_unit_size);
+
+        // Lastly, reconstruct the superblock hashes
+        MessageDigest digest = MessageDigest.getInstance("SHA-256");
+        int exefsHashRegionSize = FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x1A8) * media_unit_size;
+        byte[] exefsDataToHash = new byte[exefsHashRegionSize];
+        fNew.seek(newExefsOffset);
+        fNew.readFully(exefsDataToHash);
+        byte[] exefsSuperblockHash = digest.digest(exefsDataToHash);
+        fNew.seek(0x1C0);
+        fNew.write(exefsSuperblockHash);
+        int romfsHashRegionSize = FileFunctions.readIntFromFile(baseRom, ncchStartingOffset + 0x1B8) * media_unit_size;
+        byte[] romfsDataToHash = new byte[romfsHashRegionSize];
+        fNew.seek(newRomfsOffset);
+        fNew.readFully(romfsDataToHash);
+        byte[] romfsSuperblockHash = digest.digest(romfsDataToHash);
+        fNew.seek(0x1E0);
+        fNew.write(romfsSuperblockHash);
+
+        // While totally optional, let's zero out the NCCH signature so that
+        // it's clear this isn't a properly-signed ROM
+        byte[] zeroedSignature = new byte[0x100];
+        fNew.seek(0x0);
+        fNew.write(zeroedSignature);
+        fNew.close();
+    }
+
+    private long rebuildExefs(RandomAccessFile fNew, long newExefsOffset) throws IOException, NoSuchAlgorithmException {
+        System.out.println("NCCH: Rebuilding exefs...");
+        byte[] code = getCode();
+        if (codeCompressed) {
+            code = new BLZCoder(null).BLZ_EncodePub(code, false, true, ".code");
+        }
+
+        // Create a new ExefsFileHeader for our updated .code
+        ExefsFileHeader newCodeHeader = new ExefsFileHeader();
+        newCodeHeader.filename = codeFileHeader.filename;
+        newCodeHeader.size = code.length;
+        newCodeHeader.offset = 0;
+
+        // For all the file headers, write them to the new ROM and store them in order for hashing later
+        ExefsFileHeader[] newHeaders = new ExefsFileHeader[10];
+        newHeaders[0] = newCodeHeader;
+        fNew.seek(newExefsOffset);
+        fNew.write(newCodeHeader.asBytes());
+        for (int i = 0; i < extraExefsFiles.size(); i++) {
+            ExefsFileHeader header = extraExefsFiles.get(i);
+            newHeaders[i + 1] = header;
+            fNew.write(header.asBytes());
+        }
+
+        // Write the file data, then hash the data and write the hashes in reverse order
+        MessageDigest digest = MessageDigest.getInstance("SHA-256");
+        long endingOffset = 0;
+        for (int i = 0; i < newHeaders.length; i++) {
+            ExefsFileHeader header = newHeaders[i];
+            if (header != null) {
+                byte[] data;
+                if (header.filename.equals(".code")) {
+                    data = code;
+                } else if (header.filename.equals("icon")) {
+                    data = smdh.getBytes();
+                } else {
+                    long dataOffset = exefsOffset + 0x200 + header.offset;
+                    data = new byte[header.size];
+                    baseRom.seek(dataOffset);
+                    baseRom.readFully(data);
+                }
+                fNew.seek(newExefsOffset + 0x200 + header.offset);
+                fNew.write(data);
+                byte[] hash = digest.digest(data);
+                fNew.seek(newExefsOffset + 0x200 - ((i + 1) * 0x20));
+                fNew.write(hash);
+                endingOffset = newExefsOffset + 0x200 + header.offset + header.size;
+            }
+        }
+
+        // Pad to media unit size
+        fNew.seek(endingOffset);
+        long exefsLength = endingOffset - newExefsOffset;
+        while (exefsLength % media_unit_size != 0) {
+            fNew.writeByte(0);
+            exefsLength++;
+        }
+
+        System.out.println("NCCH: Done rebuilding exefs");
+        return exefsLength;
+    }
+
+    private long rebuildRomfs(RandomAccessFile fNew, long newRomfsOffset) throws IOException, NoSuchAlgorithmException {
+        System.out.println("NCCH: Rebuilding romfs...");
+
+        // Start by copying the romfs header straight from the original ROM. We'll update the
+        // header as we continue to build the romfs
+        byte[] romfsHeaderData = new byte[romfs_header_size];
+        baseRom.seek(romfsOffset);
+        baseRom.readFully(romfsHeaderData);
+        fNew.seek(newRomfsOffset);
+        fNew.write(romfsHeaderData);
+
+        // Now find the level 3 (file data) offset, since the first thing we need to do is write the
+        // updated file data. We're assuming here that the master hash size is smaller than the level 3
+        // hash block size, which it almost certainly will because we're not adding large amounts of data
+        // to the romfs
+        int masterHashSize = FileFunctions.readFullInt(romfsHeaderData, 0x08);
+        int level3HashBlockSize = 1 << FileFunctions.readFullInt(romfsHeaderData, 0x4C);
+        long level3Offset = romfsOffset + alignLong(0x60 + masterHashSize, level3HashBlockSize);
+        long newLevel3Offset = newRomfsOffset + alignLong(0x60 + masterHashSize, level3HashBlockSize);
+
+        // Copy the level 3 header straight from the original ROM. Since we're not adding or
+        // removing any files, the File/Directory tables should have the same offsets and lengths
+        byte[] level3HeaderData = new byte[level3_header_size];
+        baseRom.seek(level3Offset);
+        baseRom.readFully(level3HeaderData);
+        fNew.seek(newLevel3Offset);
+        fNew.write(level3HeaderData);
+
+        // Write out both hash tables and the directory metadata table. Since we're not adding or removing
+        // any files/directories, we can just use what's in the base ROM for this.
+        int directoryHashTableOffset = FileFunctions.readFullInt(level3HeaderData, 0x04);
+        int directoryHashTableLength = FileFunctions.readFullInt(level3HeaderData, 0x08);
+        int directoryMetadataTableOffset = FileFunctions.readFullInt(level3HeaderData, 0x0C);
+        int directoryMetadataTableLength = FileFunctions.readFullInt(level3HeaderData, 0x10);
+        int fileHashTableOffset = FileFunctions.readFullInt(level3HeaderData, 0x14);
+        int fileHashTableLength = FileFunctions.readFullInt(level3HeaderData, 0x18);
+        byte[] directoryHashTable = new byte[directoryHashTableLength];
+        baseRom.seek(level3Offset + directoryHashTableOffset);
+        baseRom.readFully(directoryHashTable);
+        fNew.seek(newLevel3Offset + directoryHashTableOffset);
+        fNew.write(directoryHashTable);
+        byte[] directoryMetadataTable = new byte[directoryMetadataTableLength];
+        baseRom.seek(level3Offset + directoryMetadataTableOffset);
+        baseRom.readFully(directoryMetadataTable);
+        fNew.seek(newLevel3Offset + directoryMetadataTableOffset);
+        fNew.write(directoryMetadataTable);
+        byte[] fileHashTable = new byte[fileHashTableLength];
+        baseRom.seek(level3Offset + fileHashTableOffset);
+        baseRom.readFully(fileHashTable);
+        fNew.seek(newLevel3Offset + fileHashTableOffset);
+        fNew.write(fileHashTable);
+
+        // Now reconstruct the file metadata table. It may need to be changed if any file grew or shrunk
+        int fileMetadataTableOffset = FileFunctions.readFullInt(level3HeaderData, 0x1C);
+        int fileMetadataTableLength = FileFunctions.readFullInt(level3HeaderData, 0x20);
+        byte[] newFileMetadataTable = updateFileMetadataTable(fileMetadataTableLength);
+        fNew.seek(newLevel3Offset + fileMetadataTableOffset);
+        fNew.write(newFileMetadataTable);
+
+        // Using the new file metadata table, output the file data
+        int fileDataOffset = FileFunctions.readFullInt(level3HeaderData, 0x24);
+        long endOfFileDataOffset = 0;
+        for (FileMetadata metadata : fileMetadataList) {
+            System.out.println("NCCH: Writing file " + metadata.file.fullPath + " to romfs");
+            // Users have sent us bug reports with really bizarre errors here that seem to indicate
+            // broken metadata; do this in a try-catch solely so we can log the metadata if we fail
+            try {
+                byte[] fileData;
+                if (metadata.file.fileChanged) {
+                    fileData = metadata.file.getOverrideContents();
+                } else {
+                    fileData = new byte[metadata.file.size];
+                    baseRom.seek(metadata.file.offset);
+                    baseRom.readFully(fileData);
+                }
+                long currentDataOffset = newLevel3Offset + fileDataOffset + metadata.fileDataOffset;
+                fNew.seek(currentDataOffset);
+                fNew.write(fileData);
+                endOfFileDataOffset = currentDataOffset + fileData.length;
+            } catch (Exception e) {
+                String message = String.format("Error when building romfs: File: %s, offset: %s, size: %s",
+                        metadata.file.fullPath, metadata.offset, metadata.file.size);
+                throw new RandomizerIOException(message, e);
+            }
+        }
+
+        // Now that level 3 (file data) is done, construct level 2 (hashes of file data)
+        // Note that in the ROM, level 1 comes *before* level 2, so we need to calculate
+        // level 1 length and offset as well.
+        long newLevel3EndingOffset = endOfFileDataOffset;
+        long newLevel3HashdataSize = newLevel3EndingOffset - newLevel3Offset;
+        long numberOfLevel3HashBlocks = alignLong(newLevel3HashdataSize, level3HashBlockSize) / level3HashBlockSize;
+        int level2HashBlockSize = 1 << FileFunctions.readFullInt(romfsHeaderData, 0x34);
+        long newLevel2HashdataSize = numberOfLevel3HashBlocks * 0x20;
+        long numberOfLevel2HashBlocks = alignLong(newLevel2HashdataSize, level2HashBlockSize) / level2HashBlockSize;
+        int level1HashBlockSize = 1 << FileFunctions.readFullInt(romfsHeaderData, 0x1C);
+        long newLevel1HashdataSize = numberOfLevel2HashBlocks * 0x20;
+        long newLevel1Offset = newLevel3Offset + alignLong(newLevel3HashdataSize, level3HashBlockSize);
+        long newLevel2Offset = newLevel1Offset + alignLong(newLevel1HashdataSize, level1HashBlockSize);
+        long newFileEndingOffset = alignLong(newLevel2Offset + newLevel2HashdataSize, level2HashBlockSize);
+        MessageDigest digest = MessageDigest.getInstance("SHA-256");
+        byte[] dataToHash = new byte[level3HashBlockSize];
+        for (long i = 0; i < numberOfLevel3HashBlocks; i++) {
+            fNew.seek(newLevel3Offset + (i * level3HashBlockSize));
+            fNew.readFully(dataToHash);
+            byte[] hash = digest.digest(dataToHash);
+            fNew.seek(newLevel2Offset + (i * 0x20));
+            fNew.write(hash);
+        }
+        while (fNew.getFilePointer() != newFileEndingOffset) {
+            fNew.writeByte(0);
+        }
+
+        // Now that level 2 (hashes of file data) is done, construct level 1 (hashes of
+        // hashes of file data) and the master hash/level 0 (hashes of level 1)
+        dataToHash = new byte[level2HashBlockSize];
+        for (long i = 0; i < numberOfLevel2HashBlocks; i++) {
+            fNew.seek(newLevel2Offset + (i * level2HashBlockSize));
+            fNew.readFully(dataToHash);
+            byte[] hash = digest.digest(dataToHash);
+            fNew.seek(newLevel1Offset + (i * 0x20));
+            fNew.write(hash);
+        }
+        long numberOfLevel1HashBlocks = alignLong(newLevel1HashdataSize, level1HashBlockSize) / level1HashBlockSize;
+        dataToHash = new byte[level1HashBlockSize];
+        for (long i = 0; i < numberOfLevel1HashBlocks; i++) {
+            fNew.seek(newLevel1Offset + (i * level1HashBlockSize));
+            fNew.readFully(dataToHash);
+            byte[] hash = digest.digest(dataToHash);
+            fNew.seek(newRomfsOffset + 0x60 + (i * 0x20));
+            fNew.write(hash);
+        }
+
+        // Lastly, update the header and return the size of the new romfs
+        long level1LogicalOffset = 0;
+        long level2LogicalOffset = alignLong(newLevel1HashdataSize, level1HashBlockSize);
+        long level3LogicalOffset = alignLong(level2LogicalOffset + newLevel2HashdataSize, level2HashBlockSize);
+        FileFunctions.writeFullInt(romfsHeaderData, 0x08, (int) numberOfLevel1HashBlocks * 0x20);
+        FileFunctions.writeFullLong(romfsHeaderData, 0x0C, level1LogicalOffset);
+        FileFunctions.writeFullLong(romfsHeaderData, 0x14, newLevel1HashdataSize);
+        FileFunctions.writeFullLong(romfsHeaderData, 0x24, level2LogicalOffset);
+        FileFunctions.writeFullLong(romfsHeaderData, 0x2C, newLevel2HashdataSize);
+        FileFunctions.writeFullLong(romfsHeaderData, 0x3C, level3LogicalOffset);
+        FileFunctions.writeFullLong(romfsHeaderData, 0x44, newLevel3HashdataSize);
+        fNew.seek(newRomfsOffset);
+        fNew.write(romfsHeaderData);
+        long currentLength = newFileEndingOffset - newRomfsOffset;
+        long newRomfsLength = alignLong(currentLength, media_unit_size);
+        fNew.seek(newFileEndingOffset);
+        while (fNew.getFilePointer() < newRomfsOffset + newRomfsLength) {
+            fNew.writeByte(0);
+        }
+
+        System.out.println("NCCH: Done rebuilding romfs");
+        return newRomfsLength;
+    }
+
+    private byte[] updateFileMetadataTable(int fileMetadataTableLength) {
+        fileMetadataList.sort((FileMetadata f1, FileMetadata f2) -> (int) (f1.fileDataOffset - f2.fileDataOffset));
+        byte[] fileMetadataTable = new byte[fileMetadataTableLength];
+        int currentTableOffset = 0;
+        long currentFileDataOffset = 0;
+        for (FileMetadata metadata : fileMetadataList) {
+            metadata.fileDataOffset = currentFileDataOffset;
+            if (metadata.file.fileChanged) {
+                metadata.fileDataLength = metadata.file.size;
+            }
+            byte[] metadataBytes = metadata.asBytes();
+            System.arraycopy(metadataBytes, 0, fileMetadataTable, currentTableOffset, metadataBytes.length);
+            currentTableOffset += metadataBytes.length;
+            currentFileDataOffset += metadata.fileDataLength;
+        }
+        return fileMetadataTable;
+    }
+
+    public void saveAsLayeredFS(String outputPath) throws IOException {
+        String layeredFSRootPath = outputPath + File.separator + titleId + File.separator;
+        File layeredFSRootDir = new File(layeredFSRootPath);
+        if (!layeredFSRootDir.exists()) {
+            layeredFSRootDir.mkdirs();
+        } else {
+            purgeDirectory(layeredFSRootDir);
+        }
+        String romfsRootPath = layeredFSRootPath + "romfs" + File.separator;
+        File romfsDir = new File(romfsRootPath);
+        if (!romfsDir.exists()) {
+            romfsDir.mkdirs();
+        }
+
+        if (codeChanged) {
+            byte[] code = getCode();
+            FileOutputStream fos = new FileOutputStream(new File(layeredFSRootPath + "code.bin"));
+            fos.write(code);
+            fos.close();
+        }
+
+        for (Map.Entry<String, RomfsFile> entry : romfsFiles.entrySet()) {
+            RomfsFile file = entry.getValue();
+            if (file.fileChanged) {
+                writeRomfsFileToLayeredFS(file, romfsRootPath);
+            }
+        }
+    }
+
+    private void purgeDirectory(File directory) {
+        for (File file : directory.listFiles()) {
+            if (file.isDirectory()) {
+                purgeDirectory(file);
+            }
+            file.delete();
+        }
+    }
+
+    private void writeRomfsFileToLayeredFS(RomfsFile file, String layeredFSRootPath) throws IOException {
+        String[] romfsPathComponents = file.fullPath.split("/");
+        StringBuffer buffer = new StringBuffer(layeredFSRootPath);
+        for (int i = 0; i < romfsPathComponents.length - 1; i++) {
+            buffer.append(romfsPathComponents[i]);
+            buffer.append(File.separator);
+            File currentDir = new File(buffer.toString());
+            if (!currentDir.exists()) {
+                currentDir.mkdirs();
+            }
+        }
+        buffer.append(romfsPathComponents[romfsPathComponents.length - 1]);
+        String romfsFilePath = buffer.toString();
+        FileOutputStream fos = new FileOutputStream(new File(romfsFilePath));
+        fos.write(file.getOverrideContents());
+        fos.close();
+    }
+
+    public boolean isDecrypted() throws IOException {
+        // This is the way you're *supposed* to tell if a ROM is decrypted. Specifically, this
+        // is checking the noCrypto flag on the NCCH bitflags.
+        long ncchFlagOffset = ncchStartingOffset + 0x188;
+        byte[] ncchFlags = new byte[8];
+        baseRom.seek(ncchFlagOffset);
+        baseRom.readFully(ncchFlags);
+        if ((ncchFlags[7] & 0x4) != 0) {
+            return true;
+        }
+
+        // However, some poorly-decrypted ROMs don't set this flag. So our heuristic for detecting
+        // if they're decrypted is to check whether the battle CRO exists, since all 3DS Pokemon
+        // games and updates have this file. If the game is *really* encrypted, then the odds of us
+        // successfully extracting this exact name from the metadata tables is like one in a billion.
+        return romfsFiles != null && (romfsFiles.containsKey("DllBattle.cro") || romfsFiles.containsKey("Battle.cro"));
+    }
+
+    // Retrieves a decompressed version of .code (the game's executable).
+    // The first time this is called, it will retrieve it straight from the
+    // exefs. Future calls will rely on a cached version to speed things up.
+    // If writing is enabled, it will cache the decompressed version to the
+    // tmpFolder; otherwise, it will store it in RAM.
+    public byte[] getCode() throws IOException {
+        if (!codeOpen) {
+            codeOpen = true;
+            byte[] code = new byte[codeFileHeader.size];
+
+            // File header offsets are from the start of the exefs but *exclude* the
+            // size of the exefs header, so we need to add it back ourselves.
+            baseRom.seek(exefsOffset + exefs_header_size + codeFileHeader.offset);
+            baseRom.readFully(code);
+            originalCodeCRC = FileFunctions.getCRC32(code);
+
+            if (codeCompressed) {
+                code = new BLZCoder(null).BLZ_DecodePub(code, ".code");
+            }
+
+            // Now actually make the copy or w/e
+            if (writingEnabled) {
+                File arm9file = new File(tmpFolder + ".code");
+                FileOutputStream fos = new FileOutputStream(arm9file);
+                fos.write(code);
+                fos.close();
+                arm9file.deleteOnExit();
+                this.codeRamstored = null;
+                return code;
+            } else {
+                this.codeRamstored = code;
+                byte[] newcopy = new byte[code.length];
+                System.arraycopy(code, 0, newcopy, 0, code.length);
+                return newcopy;
+            }
+        } else {
+            if (writingEnabled) {
+                return FileFunctions.readFileFullyIntoBuffer(tmpFolder + ".code");
+            } else {
+                byte[] newcopy = new byte[this.codeRamstored.length];
+                System.arraycopy(this.codeRamstored, 0, newcopy, 0, this.codeRamstored.length);
+                return newcopy;
+            }
+        }
+    }
+
+    public void writeCode(byte[] code) throws IOException {
+        if (!codeOpen) {
+            getCode();
+        }
+        codeChanged = true;
+        if (writingEnabled) {
+            FileOutputStream fos = new FileOutputStream(new File(tmpFolder + ".code"));
+            fos.write(code);
+            fos.close();
+        } else {
+            if (this.codeRamstored.length == code.length) {
+                // copy new in
+                System.arraycopy(code, 0, this.codeRamstored, 0, code.length);
+            } else {
+                // make new array
+                this.codeRamstored = null;
+                this.codeRamstored = new byte[code.length];
+                System.arraycopy(code, 0, this.codeRamstored, 0, code.length);
+            }
+        }
+    }
+
+    public boolean hasFile(String filename) {
+        return romfsFiles.containsKey(filename);
+    }
+
+    // returns null if file doesn't exist
+    public byte[] getFile(String filename) throws IOException {
+        if (romfsFiles.containsKey(filename)) {
+            return romfsFiles.get(filename).getContents();
+        } else {
+            return null;
+        }
+    }
+
+    public void writeFile(String filename, byte[] data) throws IOException {
+        if (romfsFiles.containsKey(filename)) {
+            romfsFiles.get(filename).writeOverride(data);
+        }
+    }
+
+    public void printRomDiagnostics(PrintStream logStream, NCCH gameUpdate) {
+        Path p = Paths.get(this.romFilename);
+        logStream.println("File name: " + p.getFileName().toString());
+        if (gameUpdate == null) {
+            logStream.println(".code: " + String.format("%08X", this.originalCodeCRC));
+        } else {
+            logStream.println(".code: " + String.format("%08X", gameUpdate.originalCodeCRC));
+        }
+        logStream.println("romfs header: " + String.format("%08X", this.originalRomfsHeaderCRC));
+        if (gameUpdate != null) {
+            logStream.println("romfs header (game update): " + String.format("%08X", gameUpdate.originalRomfsHeaderCRC));
+        }
+        List<String> fileList = new ArrayList<>();
+        Map<String, String> baseRomfsFileDiagnostics = this.getRomfsFilesDiagnostics();
+        Map<String, String> updateRomfsFileDiagnostics = new HashMap<>();
+        if (gameUpdate != null) {
+            updateRomfsFileDiagnostics = gameUpdate.getRomfsFilesDiagnostics();
+        }
+        for (Map.Entry<String, String> entry : updateRomfsFileDiagnostics.entrySet()) {
+            baseRomfsFileDiagnostics.remove(entry.getKey());
+            fileList.add(entry.getValue());
+        }
+        for (Map.Entry<String, String> entry : baseRomfsFileDiagnostics.entrySet()) {
+            fileList.add(entry.getValue());
+        }
+        Collections.sort(fileList);
+        for (String fileLog : fileList) {
+            logStream.println(fileLog);
+        }
+    }
+
+    public Map<String, String> getRomfsFilesDiagnostics() {
+        Map<String, String> fileDiagnostics = new HashMap<>();
+        for (Map.Entry<String, RomfsFile> entry : romfsFiles.entrySet()) {
+            if (entry.getValue().originalCRC != 0) {
+                fileDiagnostics.put(entry.getKey(), entry.getKey() + ": " + String.format("%08X", entry.getValue().originalCRC));
+            }
+        }
+        return fileDiagnostics;
+    }
+
+    public String getTmpFolder() {
+        return tmpFolder;
+    }
+
+    public RandomAccessFile getBaseRom() {
+        return baseRom;
+    }
+
+    public boolean isWritingEnabled() {
+        return writingEnabled;
+    }
+
+    public String getProductCode() {
+        return productCode;
+    }
+
+    public String getTitleId() {
+        return titleId;
+    }
+
+    public int getVersion() {
+        return version;
+    }
+
+    public static int alignInt(int num, int alignment) {
+        int mask = ~(alignment - 1);
+        return (num + (alignment - 1)) & mask;
+    }
+
+    public static long alignLong(long num, long alignment) {
+        long mask = ~(alignment - 1);
+        return (num + (alignment - 1)) & mask;
+    }
+
+    private int readVersionFromFile() {
+        try {
+            // Only CIAs can define a version in their TMD. If this is a different ROM type,
+            // just exit out early.
+            int magic = FileFunctions.readBigEndianIntFromFile(this.baseRom, ncch_and_ncsd_magic_offset);
+            if (magic == ncch_magic || magic == ncsd_magic) {
+                return 0;
+            }
+
+            // For CIAs, we need to read the title metadata (TMD) in order to retrieve the version.
+            // The TMD is after the certificate chain and ticket.
+            int certChainSize = FileFunctions.readIntFromFile(this.baseRom, 0x08);
+            int ticketSize = FileFunctions.readIntFromFile(this.baseRom, 0x0C);
+            long certChainOffset = NCCH.alignLong(cia_header_size, 64);
+            long ticketOffset = NCCH.alignLong(certChainOffset + certChainSize, 64);
+            long tmdOffset = NCCH.alignLong(ticketOffset + ticketSize, 64);
+
+            // At the start of the TMD is a signature whose length varies based on what type of signature it is.
+            int signatureType = FileFunctions.readBigEndianIntFromFile(this.baseRom, tmdOffset);
+            int signatureSize, paddingSize;
+            switch (signatureType) {
+                case 0x010003:
+                    signatureSize = 0x200;
+                    paddingSize = 0x3C;
+                    break;
+                case 0x010004:
+                    signatureSize = 0x100;
+                    paddingSize = 0x3C;
+                    break;
+                case 0x010005:
+                    signatureSize = 0x3C;
+                    paddingSize = 0x40;
+                    break;
+                default:
+                    signatureSize = -1;
+                    paddingSize = -1;
+                    break;
+            }
+            if (signatureSize == -1) {
+                // This shouldn't happen in practice, since all used and valid signature types are represented
+                // in the above switch. However, if we can't find the right signature type, then it's probably
+                // an invalid CIA anyway, so we're unlikely to get good version information out of it.
+                return 0;
+            }
+
+            // After the signature is the TMD header, which actually contains the version information.
+            long tmdHeaderOffset = tmdOffset + 4 + signatureSize + paddingSize;
+            return FileFunctions.read2ByteBigEndianIntFromFile(this.baseRom, tmdHeaderOffset + 0x9C);
+        } catch (IOException e) {
+            throw new RandomizerIOException(e);
+        }
+    }
+
+    // At the bare minimum, a 3DS game consists of what's known as a CXI file, which
+    // is just an NCCH that contains executable code. However, 3DS games are packaged
+    // in various containers that can hold other NCCH files like the game manual and
+    // firmware updates, among other things. This function's determines the location
+    // of the CXI regardless of the container.
+    public static long getCXIOffsetInFile(String filename) {
+        try {
+            RandomAccessFile rom = new RandomAccessFile(filename, "r");
+            int ciaHeaderSize = FileFunctions.readIntFromFile(rom, 0x00);
+            if (ciaHeaderSize == cia_header_size) {
+                // This *might* be a CIA; let's do our best effort to try to get
+                // a CXI out of this.
+                int certChainSize = FileFunctions.readIntFromFile(rom, 0x08);
+                int ticketSize = FileFunctions.readIntFromFile(rom, 0x0C);
+                int tmdFileSize = FileFunctions.readIntFromFile(rom, 0x10);
+
+                // If this is *really* a CIA, we'll find our CXI at the beginning of the
+                // content section, which is after the certificate chain, ticket, and TMD
+                long certChainOffset = NCCH.alignLong(ciaHeaderSize, 64);
+                long ticketOffset = NCCH.alignLong(certChainOffset + certChainSize, 64);
+                long tmdOffset = NCCH.alignLong(ticketOffset + ticketSize, 64);
+                long contentOffset = NCCH.alignLong(tmdOffset + tmdFileSize, 64);
+                int magic = FileFunctions.readBigEndianIntFromFile(rom, contentOffset + ncch_and_ncsd_magic_offset);
+                if (magic == ncch_magic) {
+                    // This CIA's content contains a valid CXI!
+                    return contentOffset;
+                }
+            }
+
+            // We don't put the following code in an else-block because there *might*
+            // exist a totally-valid CXI or CCI whose first four bytes just so
+            // *happen* to be the same as the first four bytes of a CIA file.
+            int magic = FileFunctions.readBigEndianIntFromFile(rom, ncch_and_ncsd_magic_offset);
+            rom.close();
+            if (magic == ncch_magic) {
+                // Magic is NCCH, so this just a straight-up NCCH/CXI; there is no container
+                // around the game data. Thus, the CXI offset is the beginning of the file.
+                return 0;
+            } else if (magic == ncsd_magic) {
+                // Magic is NCSD, so this is almost certainly a CCI. The CXI is always
+                // a fixed distance away from the start.
+                return 0x4000;
+            } else {
+                // This doesn't seem to be a valid 3DS file.
+                return -1;
+            }
+        } catch (IOException e) {
+            throw new RandomizerIOException(e);
+        }
+    }
+
+    private class ExefsFileHeader {
+        public String filename;
+        public int offset;
+        public int size;
+
+        public ExefsFileHeader() { }
+
+        public ExefsFileHeader(byte[] exefsHeaderData, int fileHeaderOffset) {
+            byte[] filenameBytes = new byte[0x8];
+            System.arraycopy(exefsHeaderData, fileHeaderOffset, filenameBytes, 0, 0x8);
+            this.filename = new String(filenameBytes, StandardCharsets.UTF_8).trim();
+            this.offset = FileFunctions.readFullInt(exefsHeaderData, fileHeaderOffset + 0x08);
+            this.size = FileFunctions.readFullInt(exefsHeaderData, fileHeaderOffset + 0x0C);
+        }
+
+        public boolean isValid() {
+            return this.filename != "" && this.size != 0;
+        }
+
+        public byte[] asBytes() {
+            byte[] output = new byte[0x10];
+            byte[] filenameBytes = this.filename.getBytes(StandardCharsets.UTF_8);
+            System.arraycopy(filenameBytes, 0, output, 0, filenameBytes.length);
+            FileFunctions.writeFullInt(output, 0x08, this.offset);
+            FileFunctions.writeFullInt(output, 0x0C, this.size);
+            return output;
+        }
+    }
+
+    private class DirectoryMetadata {
+        public int parentDirectoryOffset;
+        public int siblingDirectoryOffset;
+        public int firstChildDirectoryOffset;
+        public int firstFileOffset;
+        public int nextDirectoryInHashBucketOffset;
+        public int nameLength;
+        public String name;
+
+        public DirectoryMetadata(byte[] directoryMetadataBlock, int offset) {
+            parentDirectoryOffset = FileFunctions.readFullInt(directoryMetadataBlock, offset);
+            siblingDirectoryOffset = FileFunctions.readFullInt(directoryMetadataBlock, offset + 0x04);
+            firstChildDirectoryOffset = FileFunctions.readFullInt(directoryMetadataBlock, offset + 0x08);
+            firstFileOffset = FileFunctions.readFullInt(directoryMetadataBlock, offset + 0x0C);
+            nextDirectoryInHashBucketOffset = FileFunctions.readFullInt(directoryMetadataBlock, offset + 0x10);
+            nameLength = FileFunctions.readFullInt(directoryMetadataBlock, offset + 0x14);
+            name = "";
+            if (nameLength != metadata_unused) {
+                byte[] nameBytes = new byte[nameLength];
+                System.arraycopy(directoryMetadataBlock, offset + 0x18, nameBytes, 0, nameLength);
+                name = new String(nameBytes, StandardCharsets.UTF_16LE).trim();
+            }
+        }
+    }
+
+    private class FileMetadata {
+        public int offset;
+        public int parentDirectoryOffset;
+        public int siblingFileOffset;
+        public long fileDataOffset;
+        public long fileDataLength;
+        public int nextFileInHashBucketOffset;
+        public int nameLength;
+        public String name;
+        public RomfsFile file; // used only for rebuilding CXI
+
+        public FileMetadata(byte[] fileMetadataBlock, int offset) {
+            this.offset = offset;
+            parentDirectoryOffset = FileFunctions.readFullInt(fileMetadataBlock, offset);
+            siblingFileOffset = FileFunctions.readFullInt(fileMetadataBlock, offset + 0x04);
+            fileDataOffset = FileFunctions.readFullLong(fileMetadataBlock, offset + 0x08);
+            fileDataLength = FileFunctions.readFullLong(fileMetadataBlock, offset + 0x10);
+            nextFileInHashBucketOffset = FileFunctions.readFullInt(fileMetadataBlock, offset + 0x18);
+            nameLength = FileFunctions.readFullInt(fileMetadataBlock, offset + 0x1C);
+            name = "";
+            if (nameLength != metadata_unused) {
+                byte[] nameBytes = new byte[nameLength];
+                System.arraycopy(fileMetadataBlock, offset + 0x20, nameBytes, 0, nameLength);
+                name = new String(nameBytes, StandardCharsets.UTF_16LE).trim();
+            }
+        }
+
+        public byte[] asBytes() {
+            int metadataLength = 0x20;
+            if (nameLength != metadata_unused) {
+                metadataLength += alignInt(nameLength, 4);
+            }
+            byte[] output = new byte[metadataLength];
+            FileFunctions.writeFullInt(output, 0x00, this.parentDirectoryOffset);
+            FileFunctions.writeFullInt(output, 0x04, this.siblingFileOffset);
+            FileFunctions.writeFullLong(output, 0x08, this.fileDataOffset);
+            FileFunctions.writeFullLong(output, 0x10, this.fileDataLength);
+            FileFunctions.writeFullInt(output, 0x18, this.nextFileInHashBucketOffset);
+            FileFunctions.writeFullInt(output, 0x1C, this.nameLength);
+            if (!name.equals("")) {
+                byte[] nameBytes = name.getBytes(StandardCharsets.UTF_16LE);
+                System.arraycopy(nameBytes, 0, output, 0x20, nameBytes.length);
+            }
+            return output;
+        }
+    }
+}