Synology Install Git command on Synology

 

Installing git on Synology using IPKG is really easy.

Click to Read More

Install first IPKG as explained here and, in the ssh console, run next as root: ipkg install git

You can also simply install it using ipkgGui. That's even much easier than using a ssh console ;)

Now, you can use the command git in a ssh console...

Ex.: first thing you should do is to set up your name and email by typing:

git config --global user.email <your_email>
git config --global user.name <your_name>

To clone a remote projet, in a local folder,  type:

cd /<some_local_path>/

git clone https://github.com/<user-name>/<repository>.git --branch <remote_branch-name>

where "remote_branch-name" is a branch like "master", "develop", ...

The URL can be found using the "Clone or download" button of any GitHub project (See "Clone with HTTPS").

Clone GitHub Repository

Clone GitHub Repository

To update that project with a specific branch, type e.g.:

git fetch origin develop

 

Documentation can be found here.

NB.: To install Git Server, look here

Synology Synology: Expanding Volume shows no progress

I did start an expansion of my main volume by adding 2 x 3 TB, 24h ago, and looking at the progress, it's still 0%. But it seems that the display is incorrect. Looking via a console, on can see some concrete progress.

Click to Read More

If I look into the Storage Manager, I see no progress:

Expanding (Checking parity consistency 0.00%)

Expand Volume No Progress

Expand Volume No Progress

To see some progress, try the following command in a ssh console:

cat /proc/mdstat

One can see that a disk is currently resyncing and should end in xxx minutes. Another one is waiting for a resync.

Personalities : [linear] [raid0] [raid1] [raid10] [raid6] [raid5] [raid4]
md3 : active raid5 sdd7[2] sdc7[1] sdg7[0]
     1953485824 blocks super 1.2 level 5, 64k chunk, algorithm 2 [3/3] [UUU]
     [===>...............] resync = 28.7% (281233152/976742912) finish=846.3 min speed=13696K/sec
md5 : active raid5 sdd6[4] sdc6[3] sdg6[2] sdb6[1] sda6[0]
     1953485824 blocks super 1.2 level 5, 64k chunk, algorithm 2 [5/5] [UUUUU]
     resync=DELAYED
md2 : active raid5 sdd5[6] sdc5[5] sdg5[4] sdf5[3] sde5[2] sdb5[1] sda5[0]
     11692100736 blocks super 1.2 level 5, 64k chunk, algorithm 2 [7/7] [UUUUUU U]
md4 : active raid1 sdh5[0]
     3902187456 blocks super 1.2 [1/1] [U]
md1 : active raid1 sda2[0] sdb2[1] sdc2[2] sdd2[3] sde2[4] sdf2[5] sdg2[6] sdh2[ 7]
     2097088 blocks [8/8] [UUUUUUUU]
md0 : active raid1 sda1[0] sdb1[1] sdc1[2] sdd1[3] sde1[4] sdf1[5] sdg1[6] sdh1[ 7]
     2490176 blocks [8/8] [UUUUUUUU]

Synology Synology: My Own Knowledge Base

I always forget plenty of details useful to work on my Synology, such as path, tips & tricks, command or service names, etc.. So, to retrieve them more easily, I will publish them here.

Click to Read More

Post under construction...

Connect on a Synology via SSH

Synology Commands

  • Located in /usr/syno and /usr/syno/sbin resp. for binaries and script requiring root privileges
  • Interesting scripts in /usr/syno/etc.defaults/rc.sysv/ (to be used as root)
    • ./apparmor.sh {start|stop|restart|try-restart|reload|force-reload|status|kill|add_packages_profile|remove_packages_profile}
    • ./share-preapre.sh start
    • ./sftp.sh reload
    • ./tfpt.sh reload
    • ./ningx.sh reload
    • ./synomount.sh {start|stop}
    • ./pgsql.sh {start|stop|restart|reload|status}
    • ./inetd.sh { prestart_telnetd | poststop_telnetd | prestart_cups_lpd | poststop_cups_lpd }

Other command paths:

  • installed via ipkg: /opt/bin and /opt/sbin

Interesting Paths

  • Web folder: /var/services/web
    • Reference onto /volumex/web
  • Package folder: /var/packages/<Package Name>
    • See 3rd Party Packages bellow
  • Link onto all 3rd party packages
    • /usr/syno/synoman/webman/3rdparty

Synology Services

  • Names:
    • Packages' service name: pkgctl-<package>
    • Ex.: pkgctl-WebStation
    • For others, execute: /usr/syno/sbin/synoservicecfg --list
  • Config
    • path: /usr/syno/etc/synoservice.d/<service>
  •  Commands:
    • /usr/syno/sbin/synoservice --help
    • /usr/syno/sbin/synoservicecfg --help (alias of above)
    • /usr/syno/sbin/synoservicectl --help (limited features of above)
    • /usr/syno/sbin/synoservicemigrate --help
    • Ex.: synoservice --restart pkgctl-WebStation
  •  Status for Packages:
    • Each service has a file named "enabled" which is created when the service is started via the Packager Center UI (/var/packages/<package>/enabled).
    • This file is deleted once one stops the service via the Package Center UI.
    • This file is not deleted if one stops the service with the command line /usr/syno/sbin/synoservicecfg --stop pkgctl-<package>
    • This ile is not recreated if one (re)starts the service with the command line /usr/syno/sbin/synoservicecfg --start pkgctl-<package>
    • Command line ex.:
      • /usr/syno/sbin/synoservicecfg --stop "pkgctl-AudioStation"
      • output: warn: The runkey of service [pkgctl-AudioStation] has been set to "No"
      • /usr/syno/sbin/synoservicectl --stop "pkgctl-AudioStation"
      • output: pkgctl-AudioStation stoped.
  • List all Services
    • /usr/syno/sbin/synoservicecfg --list

3rd Party Packages

  • Access path: /usr/syno/synoman/webman/3rdparty/
    • This is a link to the binaries/web page/scripts of the actual application to run.
    • ls -la /usr/syno/synoman/webman/3rdpart/<packagename> will give you the actual path
  • Access Url: http://<YourNas>:<Admin Port>/webman/3rdparty/<Package Name>/....
    • To check the URL of a 3rd Party Package, simply Right Click on it in DSM's Main Menu and select "Open in new window"
  • Setup path (scripts, config, enabled "flag", INFO): /var/packages/<package>/
    • This is the location of all info used be DSM to install, access and run the package
    • Link onto the package itself /var/packages/<package>/target => /volume<x>/@appstore/<Package Name>
      • target/ is only created after the installation and can therefore not be used in Package's pre-installation script.
    • Link onto the package configuration : /var/packages/<package>/etc => /usr/syno/etc/packages/<Package Name>
      • etc/ is only created after the installation and can therefore not be used in Package's pre-installation script.
  • Installation path: /volume<x>/@appstore/<package>
    • This is the path to the binaries/web page/scripts of the application.
    • Found via: ls -la /var/packages/<package>/target
  • Configuration path: /usr/syno/etc/packages/<package>
    • This is the path where the configuration settings of the application can be stored.
    • This path is not deleted during an upgrade/uninstallation.
    • Found via: ls -la /var/packages/<package>/etc
  • List the custom feeds: cat /usr/syno/etc/packages/feeds

So, concretely, the structure of a Package Folder under /var/packages/<Package name> is like:

  • conf/
  • enabled
  • etc -> /usr/syno/etc/packages/<Package name>
  • INFO
  • scripts/
    • postinst
    • postuninst
    • postupgrade
    • preinst
    • preuninst
    • preupgrade
    • start-stop-status
  • target -> /volume<x>/@appstore/<Package name>
  • WIZARD_UIFILES/
    • install_uifile or install_uifile.sh
    • uninstall_uifile or uninstall_uifile.sh
    • upgrade_uifile or upgrade_uifile.sh
    • NB.: each file can be postfixed with the language. Ex.: install_uifile_enu or install_uifile_fre

NB: Sometimes, 'target' can be a link on -> /usr/local/packages/@appstore/<Package name>

Volumes

  • Volume Raid storage calculator: https://www.synology.com/fr-fr/support/RAID_calculator

Logs

  • Main Log path: /var/log/
  • Package installation log: /var/log/synopkg.log
  • Services log:  /var/log/synoservice.log
  • Services' path start/stop logs: /var/log/startup
  • Apache's log: /usr/local/etc/apache22/logs /usr/local/etc/apache24/logs
  • nginx's log: /var/log/nginx/

If something goes wrong and you look for information, delete all existing logs (rm -R) and redo the failing operation. Next, look for newly created logs ;)

Web Server

The Web server can be nginx, apache22 or apache24, as:

  • Configured globally in the Web Station > General Settings > HTTP back end Server or
  • Configure per Virtual Host in Web Station > Virtual Host

Config files are per Web server types:

  • Apache 22's configs are under /usr/local/etc/apache22. Ex.:
    • virtualhost config file: /usr/local/etc/apache22/sites-enabled/httpd-vhost.conf (notice: changes in this file are lost after restarting the Web Station)
    • httpd conf file:  /usr/local/etc/apache22/conf/httpd22.conf
  • Apache 24's configs are under /usr/local/etc/apache24
  • Nginx's configs are under usr/local/etc/nginx

But also in the Web Station configs:

  • Virtual Host, depending if using php56 or php 70, are also in  /var/packages/WebStation/etc/php56/conf.d/webstation_vhost.ini (notice: changes in this file are lost after restarting the Web Station)

Restart Web Server:

  • synoservicecfg --restart nginx
  • synoservice --restart pkgctl-Apache2.4
  • synoservice --restart pkgctl-WebStation

Interesting website info here.

Plex Server

  • Plex Media Server data path: /Volume<x>/Plex/Library/Application Support/Plex Media Server/
  • Complete Server Backup:
    • Stop Plex Media Server (via the Package Center)
    • Copy the directory mentioned above to backup Plex's database et configuration.
    • Restart Plex Media Server
  • Database Backup:
    • Backups are in /Volume<x>/Plex/Library/Application Support/Plex Media Server/Plug-in Support/Databases/
    • Stop Plex Media Server (via the Package Center)
    • Move away the followin file
      • com.plexapp.plugins.library.db
      • com.plexapp.plugins.library.db-shm
      • com.plexapp.plugins.library.db-wal
    • Rename the latest (or any older) com.plexapp.plugins.library.db-YYYY-MM-DD into com.plexapp.plugins.library.db
    • Restart Plex Media Server

Synology Certificates

They are (in most recent DSM version) under /usr/syno/etc/certificate/system

Synology Model

Notifications

  • Notification messages: /usr/syno/synoman/webman/texts/enu/mails
  • Notification sending mode: /usr/syno/etc/notification/notification_filter.settings
  • Other Notification messages (unknown usage): /usr/local/share/notification/dsm/enu/mails
  • Command:
    • /usr/syno/bin/synonotify <notification>  '{"[%VAR1%]": "value1", "[%VAR2%]": "value2"}'
  • Debugging:
    • syno_hibernate_debug_tool --enable 10
    • syno_hibernate_debug_tool --disable

Event Logs

  • Event messages: Events : /usr/syno/synosdk/texts/enu/events
  • Command:
    • synologset1 [sys | man | conn] [info | warn | err] eventID(%X) [substitution strings...]

Package Installation scripts

  • Documentation about installation scripts are here .
  • The etc folder of the package is a link onto /usr/syno/etc/packages/<Package Name>/
  • A script must exit 0 to succeed. Any other value will fail the installation/upgrade/uninstallation.
  • One can redirect all errors into the log with code like this:

exec 2<&-
exec 2>>/var/log/MyPackageErr.log

  • All information logged in $SYNOPKG_TEMP_LOGFILE are displayed at the end of the installation/upgrade/uninstallation in any cases (success or failure).
  • Add a <br> at the end of each line in $SYNOPKG_TEMP_LOGFILE to have a nice display. Ex.: sed -i 's/$/<br>/' "$SYNOPKG_TEMP_LOGFILE"
  • One can decide to fail an installation/upgrade/uninstallation with code like this:

if [ -s "/var/log/MyPackageErr.log" ]; then
sed -i 's/$/<br>/' "/var/log/MyPackageErr.log"
cat /var/log/MyPackageErr.log >> $SYNOPKG_TEMP_LOGFILE
exit 1
fi

 

Synology Move a Synology Package from a volume to another

I wanted to replace the smallest disks of my NAS with bigger ones. Unfortunately, some packages where installed on those. To avoid uninstalling/reinstalling everything, I did wrote a shell script which does the job, as well as a Package for Synology to offer a web interface.

Click to Read More

Here the first version of my script:

#!/bin/bash

TARGET=$1
PACKAGE=$2

if [[ $PACKAGE == "" ]]
then
	echo "Usage: mvpkg Target Package"
	echo "       Target must be like 'volumex' where x is a numeric."
	echo "       Package must be the name of a package."
	exit
fi

if [[ $TARGET != volume[0-9]* ]]
then
	echo "Usage: mvpkg Target Package"
	echo "       Target must be like 'volumex' where x is a numeric."
	echo "       Package [$PACKAGE] must be the name of a package."
	exit
fi

#Check the package and check the result: "enable" (is start), "disable" (is stop) or "does not exist"
output=$(/usr/syno/sbin/synoservicecfg --status "pkgctl-$PACKAGE" | grep Service)

if [[ $output == *"does not exist"* ]]
then
	echo "The service $PACKAGE can't be found."
	exit
else
	#find the current volume of the package and its link
	output=$( ls -la /var/packages/*/target | grep "/$PACKAGE/")
	
	link=$(echo $output | grep -oP "\/var/packages/.*/target")
	volume=$(echo $output | grep -oP "volume\d*")
	path=$(echo $output | grep -oP "\/volume.*")
	
	if [[ $link != "/var/packages/$PACKAGE/target"* ]]
	then
		echo "The service $PACKAGE is not correctly installed."
		exit
	fi
	
	if [[ $volume != "volume"* ]]
	then
		echo "The service $PACKAGE can't be located."
		exit
	fi

	if [[ $volume == $TARGET ]]
	then
		echo "The service $PACKAGE is already on $TARGET."
		exit
	fi
	
	if [[ "$path" != "/$volume/@appstore/$PACKAGE" ]]
	then
		echo "The service $PACKAGE does not have a standard location."
		exit
	fi
		
	#List Packages with dependency on this one
	#/usr/syno/sbin/synoservicecfg --reverse-dependency pkgctl-$PACKAGE
			
	#Stop the package and all its dependencies
	output=$(/usr/syno/sbin/synoservicecfg --hard-stop "pkgctl-$PACKAGE" | grep warn)
	
	if [[ $output != *"have been set"* ]]
	then
		echo "The service $PACKAGE couldn't be stopped."
		exit
	fi
	
	if [ -d "/$TARGET/@appstore/$PACKAGE" ]; then
		mv "/$TARGET/@appstore/$PACKAGE" "/$TARGET/@appstore/$PACKAGE-$(date -d "today" +"%Y%m%d%H%M").log"
	fi

	#remove the link on the previous volume
	rm -f "$link"
	
	#move the package
	mv "$path" /$TARGET/@appstore
	
	#link with the  package on the new volume
	ln -s "/$TARGET/@appstore/$PACKAGE" "$link"
	
	#Replace link also in local 
	local="/usr/local/$PACKAGE"
	if [ -L "$local" ]; then
		rm -f "$local"
		ln -s "/$TARGET/@appstore/$PACKAGE" "$local"
	fi
	
	#update settings
	sed -i "s/$volume/$TARGET/" "/usr/syno/etc/packages/$PACKAGE/*" &>/dev/null
	
	if [[ $output != *"is enabled"* ]]
	then
		echo "The service $PACKAGE didn't restart properly once moved from $volume to $TARGET."
	else	
		echo "The service $PACKAGE has been moved successfuly from $volume to $TARGET."

		#Restart packages depending on the one moved
		output=$(/usr/syno/sbin/synoservicecfg --reverse-dependency "pkgctl-$PACKAGE")

		output="$(echo $output | grep -Po "pkgctl-([^\]]*)")"
		for string in $output
		do
			/usr/syno/sbin/synoservicecfg --start "$string"
		done	
	fi	

	#Restart the package and all its dependencies
	output=$(/usr/syno/sbin/synoservicecfg --hard-start "pkgctl-$PACKAGE" | grep Service)
	
	#Check if the package has been correctly restarted
	output=$(/usr/syno/sbin/synoservicecfg --is-enabled "pkgctl-$PACKAGE")
fi

It is inspired from this post.

I did use it to move: AudioStation, CloudStation, DNSServer, NoteStation, PHP5.6, PHP7.0.

During the move, the package could temporary appear in the Package Center as needing to be repaired:

Repair Package

Repair Package444

Simply wait until the operation is completed and click next on "Refresh" in Package Center. Also, check that no other service was stopped but not restarted !! Restarting other services with dependency is not (yet) managed by the script.

WARNING: Moving some packages resulted in troubles (Packages never able to restart). Ex.: Apache Http Server 2.2 and 2.4, the Node.js, Unofficial Java Installer, WordPress. These packages did not restart properly after being moved. I still have to investigate why, but they displayed the error "failed to run the package service" for ever (even after restarting the NAS). Something I known is that there are also Symlinks onto packages in /usr/local/. My script takes those into account. But there are possibly other such dependencies somewhere else ?! Most package could fortunately be returned in their orignal state very easily by moving them back to their original volume.

Important notice

MariaDB. Before moving it, open it via the DSM main menu and change the volume where the DB files are stored.

If you wonder which package is on which volume, the easiest is to run this command in a shell: ls -la /var/packages/*/target

Troubleshooting

WordPress. After moving, it was stuck in the "repair state". I simply backuped its folder (/volumex/web/wordpress => /volumex/web/wordpress.bkp), clicked on Repair, reconfigured it to use a new DB, stopped it once fully reinstalled, deleted its new folder and replaced it with the backup (/volumex/web/wordpress.bkp => /volumex/web/wordpress) before restarting wordpress and deleting the new DB.

Node.jsFileBot-Node and the Unofficial Java Installer. I simply clicked on Repair to fix them.

Plex Media Server. during y first attempts, it didn't restart. I did simply install manually the latest version and the "update" fixed the problem without loosing any setting/library/etc... With the latest version of my script, the move succeeded.

Can't restart. Look into Package's installation path, for config files possibly still pointing at the old volume. Use for this purpose a command like:  find -L /var/packages/<package_name>/ -type f -print0 | xargs -I {} -0 grep -l "volumex" "{}"

If you find such config files, possibly update them by replacing the old volume (volumex) with the new volume (volumez) using a command like: sed -i "s/volumex/volumez/" <config_file_path>

Stuck ? If you can't stop/restart a service correctly and can update this one manually, then delete it via a console, Click next Refresh in the Package Center and reinstall it:

  • ls -la /var/packages/<package_name>/target   => this is showing you the volume<x> where it's installed
  • rm -R /var/packages/<package_name>
  • rm -R /usr/syno/etc/packages/<package_name>
  • rm -R /volume<x>/@appstore/<package_name>
  • rm -f /usr/syno/synoman/webman/3rdparty/<package_name>
  • rm -f /usr/local/<package_name>

Script & Package

I did create a "Synology Package" to be able to move packages easily from the DSM. You can find it on my own Synology Repository (See Blog's menu "SPK Server"). You will find the script in the Package if you "unzip" it, in \package\ui\mvpkg.sh

Package Mover

Package Mover

[EDIT 13-10-2017] I have added support in the package to start/stop/delete packages, display reverse and forward dependencies. Only delete a packages if you are screwed.

[EDIT 24-02-2018] The sources for my package are available on GitHub (named Package Manager).

[EDIT 23-12-2018] Since a recent update of DSM, the feature to list dependencies between packages does not work anymore.

SynologyTips Synology: "failed to install '...'. This package is not published by Synology Inc,

I got the following message when trying to install third parties packages on my Synology: "failed to install '...'. This package is not published by Synology Inc,

The solution is simply to Trust Any Publisher.

Click to Read More

Go into the "Package Center" > Settings > General tab and select "Any Publisher" in the section "Trust Level"

Trust Any Publisher

Trust Any Publisher

Tips Prolong OnePlus One Battery life by limiting charge

My OnePlus One being only used to play music via AirPlay, it's always plugged into his craddle. I knew this was not good for the battery life and started to look for an App able to prevent my mobile to reload as long as its battery was not less than a certain percentage. I found a paper recommending to reload only once the battery was lower than 25, but also recommending to no reload higher than 85%. And I found an App able to control this on many rooted android phones: "Battery Charge Limit".

Click to Read More

According to this paper, it's not good for lithium batteries' life to do cycles between full charge (100%) and full discharged (0%). Ex.: Doing cycles between 85% and 25% provides a longer service life than doing cycles between 100% and 50%.

For sure, only a full charge (100%) will provide the specified energy of the battery, and therefore its maximum runtime. So, one has to find a compromise:

  • Cycles between 75–65% offer longest life
  • Electrical Vehicles do cycles between 85–25% to prolong battery life
  • Cycles between 100–25% give long runtime, makes best use of battery, but reduces battery life.

All being linear, the life-prolonging mid-range of 85-25% reduces the energy to 60 percent.

More details on the App "Battery Charge Limit" on this blog.

Tips Easy Root Toolkit for OnePlus One

My OnePlus One is already a quite old mobile, but I am still using it at home to play music. I recently reinstall Cyanogen Mod 13 and wanted to root it as this is required to use AirAudio. To avoid doing many manual operations, I looked for a fully automated toolkit and found "Bacon Root Toolkit".

Click to Read More

Highly recommended, it works like a charm!

A demo video exists on YouTube.

Bacon Root Toolkit v1.0.3

TipsWordpress Display standard quotes in a WordPress post

Single and double quotes typed in a post are displayed by WordPress as directionnal quotes: 'blabla' or "blabla" (I.e.: left/right single/double quotes). This becomes an issue when publishing "shell scripts" samples to be copy/pasted. The solution is to type "encoded quotes". Ex.: & #39; for ' or & #34; for " (without the blanks between & and #).

Click to Read More

This is due to the WordPress converting Straight Quotes to Pretty Quotes... a feature also named Smart Quotes and due to a filter running in WordPress: the "wptexturize".

Here after, an example I used to post to illustrate how to send custom notifications from a script running on a Synology. The code was directly copy/pasted here from a shell script opened within Notepad++ (where the quotes appeared as &#39 and &#34).

/usr/syno/bin/synonotify Tag_Name '{"[%VAR1%]": "value1", "[%VAR2%]": "value2"}'

As you can see above, the single and double quotes are displayed by WordPress as symbols: '...' and "...".

The problem is that readers who copied/pasted as-is this sample in their script got execution errors. Indeed, a ' and a &#39 are not interpreted the same way within a shell.

To solve this issue, I did replace all ' and " respectively by & #39 and & #34 (without the blanks between & and #). I don't use the menu Insert > Special Character as

Another option would be to disable the "pretty-fication" feature... This can be done by opening up your theme's functions.php file and pasting the following code at the bottom right before the closing ?> PHP tag:

remove_filter('the_content', 'wptexturize');

Notice that Quotes in preformatted text (as here just above) are not replaced by Smart Quotes. But one one side, this can't be used on Quotes typed inline, and on the other side, I don't use preformatted text for my code samples...

Yet another option would be to use a plugin like the Smart Quote Fixer to remove the Smart Quotes.

But I prefer to use type the num codes as I don't want to disable Smart Quotes on the complete post...

Synology WordPress 404 on Synology after restarting NAS

Each time I restart my NAS (for update reasons), I have errors 404 when trying to reach any post of my WordPress blog, until I re-set permalinks' settings. I finally fixed it by updating my WordPress with latest Synology's package.

Click to Read More

A long time ago, rebooting my NAS started to result systematically in 404 in my WordPress blog. I found a manual fix here: simply resetting WordPress permalinks' settings was solving the problem... until the next reboot :(

But I never understood why rebooting my NAS was resulting in the lost of permalinks' settings. And could find a definitive solution.

I finally took today an hour to reproduce and further investigate the problem (motivated by the shiny sun outside :p). I found that restarting only the WordPress Package was also resulting in this issue. I noticed more precisely that the .htaccess file was deleted when starting the package (not when stopping). I am sure that removing access rights on the .htaccess file for WordPress, as described here for example, would be a solution. But the not best one.

I found the best solution by accident. A long time ago, as I was interested in a version of WordPress more recent than the one available via Synology's packages, I did a manual upgrade with the official WordPress setup. Since that time, I never did an update anymore with Synology's Package Manager, but used the native WordPress update via its own Dashboard:

WordPress-Update

Today, I did a backup of WordPress' installation folders and updated Synolgy's WordPress Package. Once the update accomplished, I noticed that the .htaccess was containing information specific to Synology:

# Synology PHP
AddHandler default-handler .htm .html .shtml
AddHandler php-fastcgi .php
AddType text/html .php
Action php-fastcgi /php56-fpm-handler.fcgi
# Synology PHP

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /wordpress/
RewriteRule ^index\.php$ - [L] RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /wordpress/index.php [L] </IfModule>

# END WordPress

And now, when restarting WordPress, the .htaccess is not deleted anymore (and permalink's settings are not lost). There is certainly a good explanation, that I ignore, but at least I won't suffer 404 anymore.

And next time I update manually WordPress, I will pay attention to backup the .htaccess as specially clearly recommended here, as well as merging that .htaccess with the updated one after the update of the Permalinks' structure:

  1. Backup your database. Read Backing Up Your Database for a detailed explanation.
  2. Backup ALL your WordPress files in your WordPress directory. Don't forget your .htaccess file.
  3. Verify the backups you created are there and usable. This is essential.
  4. Ensure first four steps are completed. Do not attempt the upgrade unless you have completed the first four steps.
  5. Delete the old WordPress files on your site, but DO NOT DELETE

    • wp-config.php file;
    • wp-content folder; Special Exception: the wp-content/cache and the wp-content/plugins/widgets folders should be deleted.
    • wp-images folder;
    • wp-includes/languages/ folder--if you are using a language file do not delete that folder;
    • .htaccess file--if you have added custom rules to your .htaccess, do not delete it;
    • robots.txt file--if your blog lives in the root of your site (ie. the blog is the site) and you have created such a file, do not delete it.
  6. Upload the new files from your computer's hard drive to the appropriate WordPress folder on your site.
  7. Run the WordPress upgrade program and follow the instructions on the screen.
  8. Update Permalinks and .htaccess. Update your Permalink Structure and merge the custom rules, if necessary, into your .htaccess file.
  9. Install updated Plugins and Themes. Please review the list of Plugins that work in Version 4.8. Check for Theme Compatibility with 4.8 and ask your Theme author for any new version.