instance_sebi is the normal installation and instance_john + share are the symlink variation like seen here:
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/srv/factorio/
βββ instance_john
βΒ Β βββ bin -> ../share/bin
βΒ Β βββ config
βΒ Β βββ data -> ../share/data
βΒ Β βββ mods
βΒ Β βββ saves
βΒ Β βββ temp
βββ instance_sebi
βΒ Β βββ bin
βΒ Β βββ config
βΒ Β βββ data
βΒ Β βββ mods
βΒ Β βββ saves
βΒ Β βββ temp
βββ share
βββ bin
βββ data
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0.000 2018-03-11 11:19:21; Factorio 0.16.28 (build 35903, linux64, headless)
0.028 Operating system: Linux (Ubuntu 16.04)
0.028 Program arguments: "/srv/factorio/instance_sebi/bin/x64/factorio" "--bind" "0.0.0.0" "--port" "34197" "--server-settings" "/srv/factorio/instance_sebi/config/server-settings.json" "--rcon-port" "43081" "--rcon-password" <private> "--start-server" "/srv/factorio/instance_sebi/saves/MP1.zip"
0.028 Read data path: /srv/factorio/instance_sebi/data
0.028 Write data path: /srv/factorio/instance_sebi [175248/207352MB]
0.028 Binaries path: /srv/factorio/instance_sebi/bin
0.034 System info: [CPU: Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz, 8 cores, RAM: 64199 MB]
0.034 Running in headless mode
...
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0.000 Error Util.cpp:49: Error configuring paths: There is no package core in /usr/share/factorio. Deduced executable directory: /srv/factorio/share/bin/x64, read data: __PATH__system-read-data__, write data: __PATH__system-write-data__
Eighter way I will leave this here Maybe someone will answer.
Edit1:
same thing happens if the symlink is absolute "/srv/factorio/share/bin" instead of relative "../share/bin"
Startup command: /srv/factorio/instance_john/bin/x64/factorio [--bind 0.0.0.0 --port 43081 --rcon-password factorio_rcon --start-server /srv/factorio/instance_john/saves/MP1.zip]
Kind regards
Sebi