I am a bit ashamed to admit I cannot find the logs. From reading 
https://wiki.gentoo.org/wiki/S6_and_s6-rc-based_init_system#logger I thought 
maybe I should be looking for file /run/uncaught-logs but could not find any 
such file in my docker instance(I understand, docker is not Gentoo).

 By default, s6-overlay containers don't have a catch-all logger, so
all the logs fall through to the container's stdout/stderr.
 You can have an in-container catch-all logger that logs to
/run/uncaught-logs if you define S6_LOGGING to 1 or 2.


While the docs did speak a lot to the directory structure used by s6, I still am finding 
it quite hard to figure out what the default directories are for some things. (e.g. I was 
clear on where my uncompiled s6-rc service directories should go but they seemed to 
"magically" get complied on boot and show up in a scan_dir)

That's a thing with s6, and even s6-rc: it does not define policies, but only mechanism. In other words: it lets you place things wherever you want,
there's no default.
Of course, higher-level software that uses the s6 bricks needs to define
policies in order to get things done; that's why s6-overlay is a set of
scripts putting directories in certain places and calling s6 binaries
with certain arguments and options.
 s6-overlay uses s6-rc-compile under the hood, so it compiles your
database for you at boot time, to keep things as simple as possible (even
though it's not the optimal way of doing it).



One additional item. As seems like not a great idea to smash the timeout for 
all services. Is there any way to adjust it on a per service basis? If not
consider me a +1 to kindly add it to a wishlist somewhere.

 You can define timeout-up and timeout-down files in your s6-rc source
definition directories, they do just that. :)


n.b. You should put up a BTC lightning "tip bucket" somewhere :)

 Thank you. Please see this Twitter thread:
 https://twitter.com/laurentbercot/status/1209247040657674240

--
 Laurent

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