IssueTracker

The issue is that Jetifier modifies jars and does not remove signatures. Below is the original class:

Classfile /tmp/non-jetified/org/bouncycastle/jce/provider/ExtCRLException.class
  Last modified Mar 1, 2015; size 362 bytes
  MD5 checksum 3968a716f9e60e1ad36c34157bd0239f
class org.bouncycastle.jce.provider.ExtCRLException extends java.security.cert.CRLException
  minor version: 0
  major version: 49
  flags: ACC_SUPER
Constant pool:
   #1 = Utf8               <init>
   #2 = Utf8               cause
   #3 = Utf8               getCause
   #4 = Utf8               java/security/cert/CRLException
   #5 = Utf8               org/bouncycastle/jce/provider/ExtCRLException
   #6 = Class              #4             // java/security/cert/CRLException
   #7 = Class              #5             // org/bouncycastle/jce/provider/ExtCRLException
   #8 = Utf8               Ljava/lang/Throwable;
   #9 = Utf8               (Ljava/lang/String;)V
  #10 = Utf8               ()Ljava/lang/Throwable;
  #11 = Utf8               (Ljava/lang/String;Ljava/lang/Throwable;)V
  #12 = NameAndType        #2:#8          // cause:Ljava/lang/Throwable;
  #13 = NameAndType        #1:#9          // "<init>":(Ljava/lang/String;)V
  #14 = Fieldref           #7.#12         // org/bouncycastle/jce/provider/ExtCRLException.cause:Ljava/lang/Throwable;
  #15 = Methodref          #6.#13         // java/security/cert/CRLException."<init>":(Ljava/lang/String;)V
  #16 = Utf8               Code
{
  java.lang.Throwable cause;
    descriptor: Ljava/lang/Throwable;
    flags:

  org.bouncycastle.jce.provider.ExtCRLException(java.lang.String, java.lang.Throwable);
    descriptor: (Ljava/lang/String;Ljava/lang/Throwable;)V
    flags:
    Code:
      stack=2, locals=3, args_size=3
         0: aload_0
         1: aload_1
         2: invokespecial #15                 // Method java/security/cert/CRLException."<init>":(Ljava/lang/String;)V
         5: aload_0
         6: aload_2
         7: putfield      #14                 // Field cause:Ljava/lang/Throwable;
        10: return

  public java.lang.Throwable getCause();
    descriptor: ()Ljava/lang/Throwable;
    flags: ACC_PUBLIC
    Code:
      stack=1, locals=1, args_size=1
         0: aload_0
         1: getfield      #14                 // Field cause:Ljava/lang/Throwable;
         4: areturn
}

One processed with Jetifier:

Classfile /tmp/jetified/org/bouncycastle/jce/provider/ExtCRLException.class
  Last modified Oct 14, 2019; size 362 bytes
  MD5 checksum 76bc557706ee3480e53d88b21316913f
class org.bouncycastle.jce.provider.ExtCRLException extends java.security.cert.CRLException
  minor version: 0
  major version: 49
  flags: ACC_SUPER
Constant pool:
   #1 = Utf8               org/bouncycastle/jce/provider/ExtCRLException
   #2 = Class              #1             // org/bouncycastle/jce/provider/ExtCRLException
   #3 = Utf8               java/security/cert/CRLException
   #4 = Class              #3             // java/security/cert/CRLException
   #5 = Utf8               cause
   #6 = Utf8               Ljava/lang/Throwable;
   #7 = Utf8               <init>
   #8 = Utf8               (Ljava/lang/String;Ljava/lang/Throwable;)V
   #9 = Utf8               (Ljava/lang/String;)V
  #10 = NameAndType        #7:#9          // "<init>":(Ljava/lang/String;)V
  #11 = Methodref          #4.#10         // java/security/cert/CRLException."<init>":(Ljava/lang/String;)V
  #12 = NameAndType        #5:#6          // cause:Ljava/lang/Throwable;
  #13 = Fieldref           #2.#12         // org/bouncycastle/jce/provider/ExtCRLException.cause:Ljava/lang/Throwable;
  #14 = Utf8               getCause
  #15 = Utf8               ()Ljava/lang/Throwable;
  #16 = Utf8               Code
{
  java.lang.Throwable cause;
    descriptor: Ljava/lang/Throwable;
    flags:

  org.bouncycastle.jce.provider.ExtCRLException(java.lang.String, java.lang.Throwable);
    descriptor: (Ljava/lang/String;Ljava/lang/Throwable;)V
    flags:
    Code:
      stack=2, locals=3, args_size=3
         0: aload_0
         1: aload_1
         2: invokespecial #11                 // Method java/security/cert/CRLException."<init>":(Ljava/lang/String;)V
         5: aload_0
         6: aload_2
         7: putfield      #13                 // Field cause:Ljava/lang/Throwable;
        10: return

  public java.lang.Throwable getCause();
    descriptor: ()Ljava/lang/Throwable;
    flags: ACC_PUBLIC
    Code:
      stack=1, locals=1, args_size=1
         0: aload_0
         1: getfield      #13                 // Field cause:Ljava/lang/Throwable;
         4: areturn
}


Changes in the constants pool cause changes in the code (indices change), which causes different MD5 checksums. This means that signatures will not match any more.

This started happening in 3.6.0-beta01 because we are using Jetifier with copyUnmodifiedLibsAlso=true flag (previously it was false).