Store messageId also in the inner message. It's avaialable in beginCryptoEncapsulation().

addon/content/pEpForThunderbird.js

@@ -664,10 +664,11 @@ class pEpForThunderbird extends pEp {
 
     // Copy some headers from the original to the new message.
     // Starting with https://pep-security.lu/dev/repos/pEp_for_Thunderbird/rev/d3c752abce8c
-    // we store the references and in-reply-to also in the inner message.
-    // Sadly at encryption time, the message ID is not yet available, so it can't be used
-    // as ID for the inner message :-(
+    // on 7th Sep 2020 in verion 1.1.006-beta we store the references and in-reply-to also
+    // in the inner message. Starting on 18th Feb. 2021 in version 1.1.101 we store the
+    // messageId in the inner message.
     if (this.currentMessage.enc_format == ENC_FORMAT_DECRYPTED) {
+      // Remove this code soon: Begin >>>>>
       if (message.id) this.currentMessage.id = message.id;
 
       // Only use original in_reply_to if decrypted (inner) message has none.
@@ -681,6 +682,7 @@ class pEpForThunderbird extends pEp {
           (typeof this.currentMessage.references !== "object" || this.currentMessage.references.length == 0)) {
         this.currentMessage.references = message.references;
       }
+      // Remove this code soon: End <<<<<
 
       // Append decryption details to internet headers in original opt_fields.
       if (message.opt_fields) {

addon/content/pEpMimeEncrypt.js

@@ -42,7 +42,8 @@ MimeEncrypt.prototype = {
   bccRecipients: null,
   replyToRecipients: null,
   originalSubject: null,
-  originalReferences: null,
+  references: null,
+  messageId: null,
   isDraftOrTemplate: false,
   passThrough: false,
 
@@ -54,16 +55,23 @@ MimeEncrypt.prototype = {
   outBuffer: "",
 
   // nsIMsgComposeSecure interface
-  requiresCryptoEncapsulation() {
+  requiresCryptoEncapsulation(msgIdentity, msgCompFields) {
     // Only if our handler was registered in pepmessengercompose.js,
     // we get here and we require encryption.
+    // Note that if `msgCompFields.subject` is set here, it will affect the
+    // subject in the message that is sent, but that is too early for us.
+    // Setting it any later has no effect.
+    // So we set the subject even earlier in pepmessengercompose.js.
     return true;
   },
 
-  beginCryptoEncapsulation(outStream, recipientList, compFields, msgIdentity, sendReport, isDraft) {
+  beginCryptoEncapsulation(outStream, recipientList, msgCompFields, msgIdentity, sendReport, isDraft) {
+    // Note that `isDraft` is false when saving as a template, so this is not useful.
     this.outStream = outStream;
     this.outStringStream = Cc["@mozilla.org/io/string-input-stream;1"].createInstance(Ci.nsIStringInputStream);
     this.inspector = Cc["@mozilla.org/jsinspector;1"].createInstance(Ci.nsIJSInspector);
+    this.references = msgCompFields.references;
+    this.messageId = msgCompFields.messageId;
 
     return null;
   },
@@ -110,14 +118,15 @@ MimeEncrypt.prototype = {
     let message = this.controller.synchronise(messagePromise);
 
     // Fill in some headers.
+    message.id = this.messageId.replace(/^<(.*)>$/, "$1");
     message.shortmsg = this.originalSubject;
     message.from = this.fromSender;
     message.to = this.toRecipients;
     message.cc = this.ccRecipients;
     message.bcc = this.bccRecipients;
     message.reply_to = this.replyToRecipients;
-    if (this.originalReferences) {
-      message.references = this.originalReferences.split(" ").map((r) => r.replace(/^<(.*)>$/, "$1"));
+    if (this.references) {
+      message.references = this.references.split(" ").map((r) => r.replace(/^<(.*)>$/, "$1"));
       message.in_reply_to = [message.references[message.references.length - 1]];
     }
 

addon/content/pepmessengercompose.js

@@ -537,8 +537,7 @@ var pEpComposer = {
                 this.getAddresses(this.win.gCurrentIdentity, compFields);
       compSec.isDraftOrTemplate = isDraftOrTemplate;
       compSec.originalSubject = compFields.subject;
-      // Note that `compFields.messageId` is empty at this point in time.
-      compSec.originalReferences = compFields.references;
+      // We deal with messageId and references in pEpMimeEncrypt.js.
       compFields.composeSecure = compSec;
 
       // This is a hack. We tell the engine whether we want protected subjects,