Mail files seem to be duplicated

[Edgar Hipp]

Hello,

I am using neomutt + offlineimap + notmuch to handle my email, but it
seems that I have a recurring issue since over a year.

The issue is that when I archive or move email, sometimes (50%
approximately), the file is still in the directory it was in at the
beginning, for example, if I want to move a file to the Archives folder,
it is still in the INBOX directory and seems to be duplicated.

I have bound `S` to archive my email with the following binding : 

```
macro index S "<enter-command>unset resolve<enter><clear-flag>N<enter-command>set resolve<enter><save-message>~/mail/bqk/Archives.2017<enter>"
```

I then hit `$` to sync my mailbox : 

```
macro index $ \
"\
<sync-mailbox>\
<enter>\
"
```

After quitting neomutt, `notmuch new` is automatically called.

However, quite often, when I enter neomutt again on the virtual mail box
bqk : I still see the message in my inbox that I have previously "Archived".

```
virtual-mailboxes "bqk" "notmuch://?query=path:bqk/** and folder:bqk/INBOX"
```

If I search for an email that had this issue : 

```
notmuch show --body=false --format=json 'subject:My custom subject'  | jq .
```

I see following result : 

```
[
  [
    [
      {
        "id": "20180209220332.1.E69088BD4579EA80 at emails.acme.co",
        "match": true,
        "excluded": false,
        "filename": [
          "/home/edgar/mail/bqk/INBOX.archive/cur/1518766879_1.2307.acme,U=4151,FMD5=6ec33b7708e41596e6d4f5707101ac47:2,S",
          "/home/edgar/mail/bqk/INBOX.archive/cur/1518766962_1.2307.acme,U=4177,FMD5=6ec33b7708e41596e6d4f5707101ac47:2,S",
          "/home/edgar/mail/bqk/INBOX.archive/cur/1518766964_1.2307.acme,U=4181,FMD5=6ec33b7708e41596e6d4f5707101ac47:2,S",
          "/home/edgar/mail/bqk/INBOX.archive/cur/1518766965_1.2307.acme,U=4183,FMD5=6ec33b7708e41596e6d4f5707101ac47:2,S",
          "/home/edgar/mail/bqk/INBOX.archive/cur/1518766966_0.2307.acme,U=4184,FMD5=6ec33b7708e41596e6d4f5707101ac47:2,S",
          "/home/edgar/mail/bqk/INBOX.archive/cur/1518767387_0.2307.acme,U=4232,FMD5=6ec33b7708e41596e6d4f5707101ac47:2,S"
        ],
        "timestamp": 1518213812,
        "date_relative": "February 09",
        "tags": [
          "inbox"
        ],
        "headers": {
          "Subject": "My custom subject",
          "From": "John doe <no-reply at acme.co>",
          "To": "jane at acme.com",
          "Date": "Fri, 09 Feb 2018 22:03:32 +0000"
        }
      },
      []
    ]
  ]
]
```

In that case, I had to archive the email 6 times until it was really
archived.

As you can see, the email has multiple "filenames". However, they all
are exactly the same (They have the exact same content, I checked with
md5sum).

I also have a running offlineimap that checks email every minute and
calls notmuch afterwards.

My idea is that in some cases, neomutt and notmuch are in a situation
where the file is copied by neomutt to its new location (in the archive
folder), but still present in the inbox directory.

Does notmuch ever write to files ?

Thanks in advance,

Edgar