# Little question about .well-known files after update

**URL:** https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932
**Category:** Support
**Tags:** update, french, english
**Created:** [September 4, 2026, 6:22pm UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932 "2026-09-04T18:22:49Z")
**Posts on this page:** 11
**Page:** 1

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### Author: ![AChess](https://forum.yunohost.org/letter_avatar_proxy/v4/letter/a/3d9bf3/32.png) [@AChess](https://forum.yunohost.org/u/AChess)
#### Post date: [September 4, 2026, 6:22pm UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/1 "2026-09-04T18:22:49Z")

</div>

### I have searched the forum for similar issues

on

### This category is for general issues(=something is broken) regarding YunoHost, _NOT_ apps.

on

### This form is written in English but feel free to write in French if you’re more comfortable!

on

### What type of hardware are you using

Old laptop or computer

### What YunoHost version are you running

12.1.40

### How are you able to access your server

The webadmin  
SSH  
Direct access via physical keyboard/screen

### Are you in a special context or did you perform specific tweaking on your YunoHost instance ?

no

### Describe your issue

Hello yunoworld ! 🙂

After doing the last update to 12.1.41 (see the log) I got several warning about /.well-known/ files being modified manually.  
I guess these files have been created when I set up the letsencrypt cert, so to me they have not been modified manually.  
This warning seems normal to me and it is probably there just to inform me that the letsencrypt config won’t get broken.  
However, just need to be sure : someone could confirm that ?

Thanks  
Alex

### Share relevant logs or error messages

[https://paste.yunohost.org/raw/azetagicox](https://paste.yunohost.org/raw/azetagicox)

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<div class="post-metadata">

### Author: ![AChess](https://forum.yunohost.org/letter_avatar_proxy/v4/letter/a/3d9bf3/32.png) [@AChess](https://forum.yunohost.org/u/AChess)
#### Post date: [September 5, 2026, 9:29am UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/2 "2026-09-05T09:29:28Z")

</div>

Salut, même message en français.

Après avoir fait la dernière mise à jour vers la 12.1.41, j’ai eu des messages d’avertissement sur les fichiers /var/www/.well-known/… qui a été modifié manuellement et ne sera pas mis à jour. Je n’ai pas modifié manuellement ces fichiers, je suppose que c’est l’autoconfig de mise en place des certificats letsencrypt qui l’a fait.

Je voulais m’assurer que cet avertissement peut tranquillement être ignoré. C’est un peu source de confusion.

Merci

Alex

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<div class="post-metadata">

### Author: ![jarod5001](https://forum.yunohost.org/user_avatar/forum.yunohost.org/jarod5001/32/5323_2.png) [@jarod5001](https://forum.yunohost.org/u/jarod5001)
#### Post date: [September 5, 2026, 10:25am UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/3 "2026-09-05T10:25:31Z")

</div>

What is the output of `yunohost tools regen-conf --dry-run --with-diff `

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<div class="post-metadata">

### Author: ![ljf](https://forum.yunohost.org/user_avatar/forum.yunohost.org/ljf/32/58_2.png) [@ljf](https://forum.yunohost.org/u/ljf)
#### Post date: [September 5, 2026, 10:51am UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/4 "2026-09-05T10:51:20Z")

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Your warning message in your log

```auto
WARNING Le fichier de configuration '/var/www/.well-known/cloud.maindomain.tld/autoconfig/mail/config-v1.1.xml' a été modifié manuellement et ne sera pas mis à jour

```

So it’s not related to let’s encrypt, that’s auto configuration files for email to let for example thunderbird autoconfigure your mailbox.

Run the command of jarod to see if something has changed or not.

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<div class="post-metadata">

### Author: ![AChess](https://forum.yunohost.org/letter_avatar_proxy/v4/letter/a/3d9bf3/32.png) [@AChess](https://forum.yunohost.org/u/AChess)
#### Post date: [September 5, 2026, 12:16pm UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/5 "2026-09-05T12:16:18Z")

</div>

Here is what I get :

```auto
WARNING Le fichier de configuration '/var/www/.well-known/grist.mydomain.tld/autoconfig/mail/config-v1.1.xml' a été modifié manuellement et ne sera pas mis à jour
WARNING Le fichier de configuration '/var/www/.well-known/snappy.mydomain.tld/autoconfig/mail/config-v1.1.xml' a été modifié manuellement et ne sera pas mis à jour
WARNING Le fichier de configuration '/var/www/.well-known/cloud.mydomain.tld/autoconfig/mail/config-v1.1.xml' a été modifié manuellement et ne sera pas mis à jour
SUCCESS La configuration aurait dû être mise à jour pour la catégorie 'dnsmasq'
dnsmasq: 
  applied: 
    /etc/dnsmasq.d/spamhaus: 
      diff: @@ -4,12 +4,12 @@
 # We pick one of spamhaus' a/b/c/d/e nameservers, cf https://multirbl.valli.org/detail/zen.spamhaus.org.html
 # And kind of hard-code the corresponding IPs because in practice dnsmasq doesn't allow to have a domain name for the resolver part of server= :| ...
 # Fun-fact : did you know that AAAA is the name of IPv6 DNS records, but also the sound you make when debugging network and DNS??? #TheMoreYouKnow
-server=/*.zen.spamhaus.org/185.15.20.108
-server=/*.zen.spamhaus.org/208.85.20.147
+server=/*.zen.spamhaus.org/147.102.226.131
+server=/*.zen.spamhaus.org/185.82.216.38
 server=/*.zen.spamhaus.org/213.81.185.73
+server=/*.zen.spamhaus.org/217.12.210.137
 server=/*.zen.spamhaus.org/2a00:12a8:8000::fff0:3
 server=/*.zen.spamhaus.org/2a05:9404::e0
 server=/*.zen.spamhaus.org/2a05:f480:2000:1246:9998:cf46:6cf8:1e7a
-server=/*.zen.spamhaus.org/2a05:f480:2800:129f:da1e:3a4f:abe5:3481
 server=/*.zen.spamhaus.org/70.34.211.66
 server=/*.zen.spamhaus.org/82.118.21.219
      status: updated
  pending: 
nginx: 
  applied: 
  pending: 
    /var/www/.well-known/cloud.mydomain.tld/autoconfig/mail/config-v1.1.xml: 
      diff: @@ -1,19 +0,0 @@
-<clientConfig version="1.1">
- <emailProvider id="cloud.mydomain.tld">
- <domain>cloud.mydomain.tld</domain>
- <incomingServer type="imap">
- <hostname>cloud.mydomain.tld</hostname>
- <port>993</port>
- <socketType>SSL</socketType>
- <authentication>password-cleartext</authentication>
- <username>%EMAILLOCALPART%</username>
- </incomingServer>
- <outgoingServer type="smtp">
- <hostname>cloud.mydomain.tld</hostname>
- <port>587</port>
- <socketType>STARTTLS</socketType>
- <authentication>password-cleartext</authentication>
- <username>%EMAILLOCALPART%</username>
- </outgoingServer>
- </emailProvider>
-</clientConfig>
      status: modified
    /var/www/.well-known/grist.mydomain.tld/autoconfig/mail/config-v1.1.xml: 
      diff: @@ -1,19 +0,0 @@
-<clientConfig version="1.1">
- <emailProvider id="grist.mydomain.tld">
- <domain>grist.mydomain.tld</domain>
- <incomingServer type="imap">
- <hostname>grist.mydomain.tld</hostname>
- <port>993</port>
- <socketType>SSL</socketType>
- <authentication>password-cleartext</authentication>
- <username>%EMAILLOCALPART%</username>
- </incomingServer>
- <outgoingServer type="smtp">
- <hostname>grist.mydomain.tld</hostname>
- <port>587</port>
- <socketType>STARTTLS</socketType>
- <authentication>password-cleartext</authentication>
- <username>%EMAILLOCALPART%</username>
- </outgoingServer>
- </emailProvider>
-</clientConfig>
      status: modified
    /var/www/.well-known/snappy.mydomain.tld/autoconfig/mail/config-v1.1.xml: 
      diff: @@ -1,19 +0,0 @@
-<clientConfig version="1.1">
- <emailProvider id="snappy.mydomain.tld">
- <domain>snappy.mydomain.tld</domain>
- <incomingServer type="imap">
- <hostname>snappy.mydomain.tld</hostname>
- <port>993</port>
- <socketType>SSL</socketType>
- <authentication>password-cleartext</authentication>
- <username>%EMAILLOCALPART%</username>
- </incomingServer>
- <outgoingServer type="smtp">
- <hostname>snappy.mydomain.tld</hostname>
- <port>587</port>
- <socketType>STARTTLS</socketType>
- <authentication>password-cleartext</authentication>
- <username>%EMAILLOCALPART%</username>
- </outgoingServer>
- </emailProvider>
-</clientConfig>
      status: modified

```

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<div class="post-metadata">

### Author: ![tmb](https://forum.yunohost.org/letter_avatar_proxy/v4/letter/t/7c8e57/32.png) [@tmb](https://forum.yunohost.org/u/tmb)
#### Post date: [September 5, 2026, 12:58pm UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/6 "2026-09-05T12:58:24Z")

</div>

Sorry, it’s only in english, but I think `autoconfig/mail/config-v1.1.xml` generation is buggy.

The file is missing a final “newline” and when the email in/out feature is disabled it is not removed. The left-over then triggers a “manually modified” error.

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<div class="post-metadata">

### Author: ![AChess](https://forum.yunohost.org/letter_avatar_proxy/v4/letter/a/3d9bf3/32.png) [@AChess](https://forum.yunohost.org/u/AChess)
#### Post date: [September 5, 2026, 1:15pm UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/7 "2026-09-05T13:15:02Z")

</div>

Oh thanks, so you’re saying that it is a problem with the way yunohost manage the email in the domain section ? Indeed I disabled the mail for all my subdomain.

Any advice on how to fix that ?

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<div class="post-metadata">

### Author: ![tmb](https://forum.yunohost.org/letter_avatar_proxy/v4/letter/t/7c8e57/32.png) [@tmb](https://forum.yunohost.org/u/tmb)
#### Post date: [September 5, 2026, 2:19pm UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/8 "2026-09-05T14:19:41Z")

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If you have the possibility please file a bug.

I think `sudo yunohost tools regen-conf --with-diff --force nginx` might overwrite/remove these files.

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<div class="post-metadata">

### Author: ![AChess](https://forum.yunohost.org/letter_avatar_proxy/v4/letter/a/3d9bf3/32.png) [@AChess](https://forum.yunohost.org/u/AChess)
#### Post date: [September 5, 2026, 2:25pm UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/9 "2026-09-05T14:25:31Z")

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Thanks again, it seems good.

I’ll have a look on how to file bug.

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<div class="post-metadata">

### Author: ![ljf](https://forum.yunohost.org/user_avatar/forum.yunohost.org/ljf/32/58_2.png) [@ljf](https://forum.yunohost.org/u/ljf)
#### Post date: [September 6, 2026, 11:50am UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/10 "2026-09-06T11:50:24Z")

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The bug is already reported [Cannot disable email for domain without generating constant warnings · Issue #2515 · YunoHost/issues · GitHub](https://github.com/YunoHost/issues/issues/2515)

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<div class="post-metadata">

### Author: ![system](https://forum.yunohost.org/uploads/default/original/2X/f/f59fe8e3ee6b100b4f574d30d6e30479c68b89f0.png) [@system](https://forum.yunohost.org/u/system)
#### Post date: [October 6, 2026, 11:50am UTC](https://forum.yunohost.org/t/little-question-about-well-known-files-after-update/42932/11 "2026-10-06T11:50:26Z")

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