Fix -o <app>.apk writing the input archive into classes.dex

[monperrus]

Running simplify some.apk -o out.apk produces an out.apk whose classes.dex entry is the input APK, not the simplified dex — the output is unusable.

Cause

The option parser sets the output file while iterating over the flags, i.e. SimplifyOptions.setOutFile() runs before setInFile() is called with the positional input path. setOutFile() picks outDexFile based on isZip():

void setOutFile(File outFile) {
    this.outFile = outFile;
    if (isZip()) {
        outDexFile = File.createTempFile("simplify", "dex"); // temp, grafted into the apk later
    } else {
        outDexFile = outFile;
    }
}

But at that point inputType is still null, so isZip() is false and outDexFile is set to outFile itself. For a zip input the Launcher then does:

dexBuilder.writeTo(outDexFile);                 // writes a real dex to out.apk
Files.copy(inFile, outFile, REPLACE_EXISTING);  // overwrites out.apk with the input apk
updateZip(outFile, outDexFile, "classes.dex");  // outDexFile == outFile

so it copies the input APK into the output archive's classes.dex entry.

Fix

Recompute the out dex file in setInFile() once the input type is known (only when an output file was already set), so a zip input gets a distinct temp dex again.

Verification

Before: unzip -p out.apk classes.dex | file - → Zip archive data (the input APK).
After: unzip -p out.apk classes.dex | file - → Dalvik dex file version 035.