Gradle plugin creates fat jars that do not align with unspecified assumption that META-INF/MANIFEST.MF should be the first or second entry

[DanielThomas]

The boot jars produced by the Gradle plugin injects the launcher classes first, violating an implicit specification discussed here and in JarInputStream:

https://bugs.openjdk.java.net/browse/JDK-8031748

    public JarInputStream(InputStream in, boolean verify) throws IOException {
        super(in);
        this.doVerify = verify;

        // This implementation assumes the META-INF/MANIFEST.MF entry
        // should be either the first or the second entry (when preceded
        // by the dir META-INF/). It skips the META-INF/ and then
        // "consumes" the MANIFEST.MF to initialize the Manifest object.

In our case we're indexing jars from in a context where we don't have random access to the file, so that implicit contract makes it easy to know if we can expect a manifest or if we need to fallback, but it's not possible for these jars:

  Length      Date    Time    Name
---------  ---------- -----   ----
        0  2019-02-15 10:26   org/
        0  2019-02-15 10:26   org/springframework/
        0  2019-02-15 10:26   org/springframework/boot/
        0  2019-02-15 10:26   org/springframework/boot/loader/
        0  2019-02-15 10:26   org/springframework/boot/loader/data/
        0  2019-02-15 10:26   org/springframework/boot/loader/jar/
        0  2019-02-15 10:26   org/springframework/boot/loader/archive/
        0  2019-02-15 10:26   org/springframework/boot/loader/util/
     2688  2019-02-15 10:26   org/springframework/boot/loader/data/RandomAccessDataFile$DataInputStream.class
     5267  2019-02-15 10:26   org/springframework/boot/loader/jar/CentralDirectoryFileHeader.class
     3263  2019-02-15 10:26   org/springframework/boot/loader/data/RandomAccessDataFile$FileAccess.class
     1487  2019-02-15 10:26   org/springframework/boot/loader/archive/ExplodedArchive$FileEntryIterator$EntryComparator.class
     3837  2019-02-15 10:26   org/springframework/boot/loader/archive/ExplodedArchive$FileEntryIterator.class
      282  2019-02-15 10:26   org/springframework/boot/loader/data/RandomAccessDataFile$1.class
     3116  2019-02-15 10:26   org/springframework/boot/loader/jar/CentralDirectoryEndRecord.class
    11548  2019-02-15 10:26   org/springframework/boot/loader/jar/Handler.class
     5243  2019-02-15 10:26   org/springframework/boot/loader/archive/ExplodedArchive.class
     4015  2019-02-15 10:26   org/springframework/boot/loader/data/RandomAccessDataFile.class
     4624  2019-02-15 10:26   org/springframework/boot/loader/jar/CentralDirectoryParser.class
     1813  2019-02-15 10:26   org/springframework/boot/loader/jar/ZipInflaterInputStream.class
      302  2019-02-15 10:26   org/springframework/boot/loader/archive/Archive$Entry.class
      273  2019-02-15 10:26   org/springframework/boot/loader/archive/ExplodedArchive$1.class
      485  2019-02-15 10:26   org/springframework/boot/loader/data/RandomAccessData.class
      437  2019-02-15 10:26   org/springframework/boot/loader/archive/Archive$EntryFilter.class
     7336  2019-02-15 10:26   org/springframework/boot/loader/archive/JarFileArchive.class
     1953  2019-02-15 10:26   org/springframework/boot/loader/PropertiesLauncher$PrefixMatchingArchiveFilter.class
     1484  2019-02-15 10:26   org/springframework/boot/loader/PropertiesLauncher$ArchiveEntryFilter.class
      266  2019-02-15 10:26   org/springframework/boot/loader/PropertiesLauncher$1.class
    19737  2019-02-15 10:26   org/springframework/boot/loader/PropertiesLauncher.class
     4684  2019-02-15 10:26   org/springframework/boot/loader/Launcher.class
     1502  2019-02-15 10:26   org/springframework/boot/loader/MainMethodRunner.class
     3608  2019-02-15 10:26   org/springframework/boot/loader/ExecutableArchiveLauncher.class
     1721  2019-02-15 10:26   org/springframework/boot/loader/WarLauncher.class
     1585  2019-02-15 10:26   org/springframework/boot/loader/JarLauncher.class
     5203  2019-02-15 10:26   org/springframework/boot/loader/util/SystemPropertyUtils.class
     1535  2019-02-15 10:26   org/springframework/boot/loader/LaunchedURLClassLoader$UseFastConnectionExceptionsEnumeration.class
     5699  2019-02-15 10:26   org/springframework/boot/loader/LaunchedURLClassLoader.class
      616  2019-02-15 10:26   org/springframework/boot/loader/jar/Bytes.class
      702  2019-02-15 10:26   org/springframework/boot/loader/jar/JarURLConnection$1.class
     1779  2019-02-15 10:26   org/springframework/boot/loader/archive/JarFileArchive$EntryIterator.class
     4306  2019-02-15 10:26   org/springframework/boot/loader/jar/JarURLConnection$JarEntryName.class
     1081  2019-02-15 10:26   org/springframework/boot/loader/archive/JarFileArchive$JarFileEntry.class
     9854  2019-02-15 10:26   org/springframework/boot/loader/jar/JarURLConnection.class
      945  2019-02-15 10:26   org/springframework/boot/loader/archive/Archive.class
     1233  2019-02-15 10:26   org/springframework/boot/loader/jar/JarFile$2.class
     2062  2019-02-15 10:26   org/springframework/boot/loader/jar/JarFile$1.class
     1374  2019-02-15 10:26   org/springframework/boot/loader/jar/JarFile$JarFileType.class
    15076  2019-02-15 10:26   org/springframework/boot/loader/jar/JarFile.class
     4976  2019-02-15 10:26   org/springframework/boot/loader/jar/AsciiBytes.class
     1593  2019-02-15 10:26   org/springframework/boot/loader/jar/JarFileEntries$1.class
     2046  2019-02-15 10:26   org/springframework/boot/loader/jar/JarFileEntries$EntryIterator.class
      540  2019-02-15 10:26   org/springframework/boot/loader/jar/CentralDirectoryVisitor.class
      299  2019-02-15 10:26   org/springframework/boot/loader/jar/JarEntryFilter.class
     3619  2019-02-15 10:26   org/springframework/boot/loader/jar/JarEntry.class
      345  2019-02-15 10:26   org/springframework/boot/loader/jar/FileHeader.class
     3650  2019-02-15 10:26   org/springframework/boot/loader/jar/StringSequence.class
    14087  2019-02-15 10:26   org/springframework/boot/loader/jar/JarFileEntries.class
     1102  2019-02-15 10:26   org/springframework/boot/loader/archive/ExplodedArchive$FileEntry.class
        0  2019-04-30 01:41   META-INF/
      858  2019-04-30 01:41   META-INF/MANIFEST.MF

In the meantime we're going to have our code check for this case specifically.