Compiling the amalgamator with linux gives (easy to fix):
kraken@roxxorx ~/Projects/juce/extras/amalgamator/Builds/Linux $ make
Linking Amalgamator
build/intermediate/Debug/JuceLibraryCode.o: In function `~OggVorbisAudioFormat':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:401: undefined reference to `juce::AudioFormat::~AudioFormat()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:401: undefined reference to `juce::AudioFormat::~AudioFormat()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:401: undefined reference to `juce::AudioFormat::~AudioFormat()'
build/intermediate/Debug/JuceLibraryCode.o: In function `~FlacAudioFormat':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:488: undefined reference to `juce::AudioFormat::~AudioFormat()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:488: undefined reference to `juce::AudioFormat::~AudioFormat()'
build/intermediate/Debug/JuceLibraryCode.o:/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:488: more undefined references to `juce::AudioFormat::~AudioFormat()' follow
build/intermediate/Debug/JuceLibraryCode.o: In function `OggVorbisAudioFormat':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:395: undefined reference to `juce::AudioFormat::AudioFormat(juce::String const&, wchar_t const**)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:395: undefined reference to `juce::AudioFormat::AudioFormat(juce::String const&, wchar_t const**)'
build/intermediate/Debug/JuceLibraryCode.o: In function `FlacAudioFormat':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:482: undefined reference to `juce::AudioFormat::AudioFormat(juce::String const&, wchar_t const**)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:482: undefined reference to `juce::AudioFormat::AudioFormat(juce::String const&, wchar_t const**)'
build/intermediate/Debug/JuceLibraryCode.o: In function `juce::FlacReader::useMetadata(FlacNamespace::FLAC__StreamMetadata_StreamInfo const&)':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:149: undefined reference to `juce::AudioSampleBuffer::setSize(int, int, bool, bool, bool)'
build/intermediate/Debug/JuceLibraryCode.o: In function `juce::FlacReader::useSamples(int const* const*, int)':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:228: undefined reference to `juce::AudioSampleBuffer::setSize(int, int, bool, bool, bool)'
build/intermediate/Debug/JuceLibraryCode.o: In function `~OggReader':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:132: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
build/intermediate/Debug/JuceLibraryCode.o: In function `~OggWriter':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:335: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:335: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:335: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:335: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
build/intermediate/Debug/JuceLibraryCode.o: In function `juce::OggReader::readSamples(int**, int, int, long long, int)':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:199: undefined reference to `juce::AudioSampleBuffer::clear(int, int)'
build/intermediate/Debug/JuceLibraryCode.o: In function `~FlacReader':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:140: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
build/intermediate/Debug/JuceLibraryCode.o: In function `~FlacWriter':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:357: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:357: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:357: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:357: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
build/intermediate/Debug/JuceLibraryCode.o: In function `OggReader':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:104: undefined reference to `juce::AudioFormatReader::AudioFormatReader(juce::InputStream*, juce::String const&)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:104: undefined reference to `juce::AudioSampleBuffer::AudioSampleBuffer(int, int)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:125: undefined reference to `juce::AudioSampleBuffer::setSize(int, int, bool, bool, bool)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:127: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:127: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
build/intermediate/Debug/JuceLibraryCode.o: In function `FlacWriter':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:324: undefined reference to `juce::AudioFormatWriter::AudioFormatWriter(juce::OutputStream*, juce::String const&, double, unsigned int, unsigned int)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:341: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
build/intermediate/Debug/JuceLibraryCode.o: In function `FlacReader':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:105: undefined reference to `juce::AudioFormatReader::AudioFormatReader(juce::InputStream*, juce::String const&)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:105: undefined reference to `juce::AudioSampleBuffer::AudioSampleBuffer(int, int)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:135: undefined reference to `juce::AudioSampleBuffer::~AudioSampleBuffer()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_FlacAudioFormat.cpp:135: undefined reference to `juce::AudioFormatReader::~AudioFormatReader()'
build/intermediate/Debug/JuceLibraryCode.o: In function `OggWriter':
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:269: undefined reference to `juce::AudioFormatWriter::AudioFormatWriter(juce::OutputStream*, juce::String const&, double, unsigned int, unsigned int)'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:282: undefined reference to `juce::JUCEApplication::getInstance()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:284: undefined reference to `juce::JUCEApplication::getInstance()'
/home/kraken/Projects/juce/extras/amalgamator/Builds/Linux/../../JuceLibraryCode/../../../amalgamation/../src/audio/audio_file_formats/juce_OggVorbisAudioFormat.cpp:312: undefined reference to `juce::AudioFormatWriter::~AudioFormatWriter()'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTVN4juce20OggVorbisAudioFormatE[vtable for juce::OggVorbisAudioFormat]+0x10): undefined reference to `juce::AudioFormat::canHandleFile(juce::File const&)'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTVN4juce15FlacAudioFormatE[vtable for juce::FlacAudioFormat]+0x10): undefined reference to `juce::AudioFormat::canHandleFile(juce::File const&)'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTVN4juce15FlacAudioFormatE[vtable for juce::FlacAudioFormat]+0x28): undefined reference to `juce::AudioFormat::getQualityOptions()'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTIN4juce20OggVorbisAudioFormatE[typeinfo for juce::OggVorbisAudioFormat]+0x8): undefined reference to `typeinfo for juce::AudioFormat'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTIN4juce15FlacAudioFormatE[typeinfo for juce::FlacAudioFormat]+0x8): undefined reference to `typeinfo for juce::AudioFormat'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTIN4juce9OggWriterE[typeinfo for juce::OggWriter]+0x8): undefined reference to `typeinfo for juce::AudioFormatWriter'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTVN4juce9OggReaderE[vtable for juce::OggReader]+0x10): undefined reference to `juce::AudioFormatReader::readMaxLevels(long long, long long, float&, float&, float&, float&)'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTIN4juce9OggReaderE[typeinfo for juce::OggReader]+0x8): undefined reference to `typeinfo for juce::AudioFormatReader'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTIN4juce10FlacWriterE[typeinfo for juce::FlacWriter]+0x8): undefined reference to `typeinfo for juce::AudioFormatWriter'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTVN4juce10FlacReaderE[vtable for juce::FlacReader]+0x10): undefined reference to `juce::AudioFormatReader::readMaxLevels(long long, long long, float&, float&, float&, float&)'
build/intermediate/Debug/JuceLibraryCode.o:(.rodata._ZTIN4juce10FlacReaderE[typeinfo for juce::FlacReader]+0x8): undefined reference to `typeinfo for juce::AudioFormatReader'
collect2: ld returned 1 exit status
make: *** [build/amalgamator] Error 1
probably there should be a way to handle 3rd party libraries and automatically find which ones to link in jucer itself.