refactor: nested dex + replace --only-main-classes with -a/--all-src

[IgorEisberg]

Fixes: #4068

• Change default mode for mDecodeSources from FULL to ONLY_MAIN_CLASSES, which is more common in normal usage.
• Replace --only-main-classes with -a/--all-src as it's less common in normal usage, and complements -s/--no-src.
• Add CLASSES_FILES_PATTERN to easily separate standard dex files from unknown dex files (usually loaded dynamically by the app).
• With -a/--all-src, unknown dex files are (not matching CLASSES_FILES_PATTERN) decoded and not copied to the working folder.
• Without -a/--all-src, unknown dex files are copied to the unknown folder to be repacked as-is.
• Fix decoding nested dex files by using @ as a path separator placeholder in smali_ folder name.
• Rename DuplicateDexTest to DynamicDexTest as "duplicate" dex are now impossible (unless these dex file have @ in their name, for some reason). Now it tests for success rather than validating an old bug that caused failure.

Misc optimizations:

• Rename ResourcesDecoder to ResDecoder for simplicity and to match variable names.
• Instantiate SmaliDecoder once and make it reusable, like ResDecoder.
• Separation of concerns: Let SmaliDecoder record handled mDexFiles and the minimal mInferredApiLevel to be later used by ApkDecoder.
• Change condition for saving inferred API level from "if no resources" to "if no manifest or if decoded without resources", as minSdkVersion is only decoded from AndroidManifest.xml, not resources.arsc.
• Instantiate SmaliBuilder once and make it reusable.
• Instantiate AaptInvoker once for consistency with ResDecoder.
• Optimize Directory by using separator (String) and separatorChar (char), like File class, to avoid concatenation of different data types by an implicit StringBuilder.
• Use some shorter variable names for readability, like RAW_DIRS, *_FILES_PATTERN, resFileMap and resZip.
• Normalized test APK names with underscores for consistency.
• Removed unnecessary sConfig.setForced(true) in tests, use separate folders instead for easier analysis in case of failure.
• Some minor cleanup.

[Copilot]

Pull request overview

This PR refactors the handling of nested/dynamic dex files and replaces the --only-main-classes CLI option with -a/--all-src. The default decoding mode changes from decoding all sources to only decoding standard classes*.dex files, which is more typical for normal usage. Dynamic dex files (not matching the classes*.dex pattern) are now handled differently: with -a they're decoded, without it they're copied to the "unknown" folder. The PR also fixes nested dex file decoding by using @ as a path separator placeholder in smali folder names.

Changes:

• Default decode mode changed from FULL to ONLY_MAIN_CLASSES; CLI option inverted from --only-main-classes to -a/--all-src
• Nested dex files supported by replacing path separators with @ in folder names during decode, reversed during build
• SmaliDecoder and SmaliBuilder refactored to be reusable across multiple dex files

Reviewed changes

Copilot reviewed 23 out of 27 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
brut.j.dir/.../Directory.java	Added separatorChar constant alongside separator String for performance
brut.j.dir/.../AbstractDirectory.java	Uses separatorChar for indexOf operations
brut.j.dir/.../ZipRODirectory.java	Uses separatorChar for indexOf operations
brut.apktool/.../Config.java	Changed default mDecodeSources from FULL to ONLY_MAIN_CLASSES
brut.apktool/.../ApkInfo.java	Added CLASSES_FILES_PATTERN, renamed constants for clarity
brut.apktool/.../SmaliDecoder.java	Made reusable with thread-safe mDexFiles tracking
brut.apktool/.../SmaliBuilder.java	Made reusable by accepting smaliDir parameter instead of storing it
brut.apktool/.../ResDecoder.java	Renamed from ResourcesDecoder for brevity
brut.apktool/.../ResFileDecoder.java	Renamed resFileMapping to resFileMap
brut.apktool/.../AaptInvoker.java	Removed conditional check for resources.zip existence
brut.apktool/.../ApkDecoder.java	Refactored dex handling with @ separator for nested paths
brut.apktool/.../ApkBuilder.java	Reverse @ separator back to path separator during build
brut.apktool/.../Main.java	Replaced --only-main-classes with -a/--all-src CLI option
brut.apktool/.../TestUtils.java	Optimized replace operations
brut.apktool/.../test/*.java	Renamed test resources, removed setForced(true), use separate output dirs
test resources/*.apk	Renamed test APK files with underscores for consistency

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[iBotPeaches]

Can you hit PR for the doc changes?

[IgorEisberg]

Can you hit PR for the doc changes?

Done!