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I'm not sure why it needs to do anything regarding ownership or ACLs. If you aren't running as an elevated process then you cannot take ownership, but even if you could, I'm not sure why it tries to make the files writable for all users. If two users need to edit on the same machine, you would just put the game folder somewhere where they can both write and take the default inheritance from that location, and if someone does set an ACL you wouldn't want to have the build process modify it.

If you search around the forum a bit you'll find a couple of people who have implemented a replacement engine, although they are work in progress:

https://github.com/tzachshabtay/MonoAGS (C#)
https://github.com/CalinLeafshade/adore (Lua)

There is currently an effort underway to cleanup the existing code, removing a lot of legacy components, so you may want to have a read here.

It looks like you can force applications to default to the higher performance options by exporting a flag that the driver looks for.

I would imagine the CPU and GPU share a heatsink, it might have just been an issue with Parallels.
http://kb.parallels.com/en/123268

I had the stuttering issue on room change when I used Windows 7, but the same games were fine once using Windows 10. I also thought it was a graphics driver issue, as I would get some general performance issues with anything using Direct3D. Using the threaded audio mode would fix it, or using WAV files for audio, so I think the issue was that the buffer for MP3 and OGG decoding wasn't updating before the next engine tick.

I'm curious if there are any updates on the issue that the DirectX 9 driver doesn't work on certain Windows 10 systems?

I've not tested it out, but apparently installing the full DirectX 9 runtime package can restore compatibility with Windows 10.
https://www.microsoft.com/en-us/download/details.aspx?id=8109

Inkscape is more about vector graphics, although you can always convert your final images to bitmaps.
You might like GrafX2 if you want to go retro (very brush centric and only a 256 colour palette). There are some good tutorials for the basics on YouTube.

Since the CHM format was reverse engineered you can also get the HTML files from the CHM file, by extracting it with 7-zip.

I'm pretty sure it is off by default, as originally it wasn't supported when using Direct3D.

It looks like there is a problem with the SSL certificate, it seems to issued for the wrong hostnames (rwdb.info and www.rwdb.info).
https://www.ssllabs.com/ssltest/analyze.html?d=www.adventuregamestudio.co.uk&hideResults=on

Windows Defender in Windows 10 incorporates what was previously Security Essentials. It's full realtime anti-virus supplied by the OS vendor. If you want to install something else that replaces or bypasses built-in OS protection and uses its own you can do, but this also has the ability to make the situation a lot worse.
https://googleprojectzero.blogspot.co.uk/2016/06/how-to-compromise-enterprise-endpoint.html

If you don't want real-time scanning, ClamAV is free and cross-platform.
Personally, I would ignore any stats you read on detection rates.
For Windows 7, I would just install Security Essentials.

The archive that is used to distribute the game needs to preserve the execute bit on what should be executable, but because the game is compiled on Windows the execute bit won't be available to set and compression utilities on Windows will usually ignore it. So you would have to have a game build option which writes directly to an archive and flags which files should be executable within that archive (most likely extended headers in a zip file, or a standard tar file).

I downloaded the Linux version from both sites, and it looks like your builds are missing the engine components.
It's probably this: https://www.adventuregamestudio.co.uk/forums/index.php?opic=53933.msg636550939#msg636550939.

It sounds a lot like this:
http://askubuntu.com/questions/492467/sound-problems-in-ubuntu-14-04

You could try removing your pulseaudio configuration or try to set the default format and sample rate:
http://manpages.ubuntu.com/manpages/trusty/man5/pulse-daemon.conf.5.html

Unofficially, I would say that you will get less rendering issues with the native port but you need a decent-ish CPU to cover the scaling overhead. I've used it with a few different desktop environments and also built and used it on PowerPC, it's been fine in most cases. I've not tried with Hi-DPI though.

I've tried the build that you linked. For me, sometimes the change between the modes doesn't work every time. Sometimes it works fine, but I've had it go in circles (seems to be switching and then switching back in a loop) trying to go from fullscreen to a window. I had to press CTL+ALT+DEL to make it stop, at which point it did switch to a window and stay in windowed mode. I've also seen it fail to go fullscreen (seems to change and then instantly change back, but didn't do it continuously). This is using Direct3D.

I would suggest testing with headphones; It sounds a lot like what would happen if the mixer output is getting turned down because input is detected on a microphone input.

I think it's a side effect of using a blocking function, so until the blocking is finished, "Lose" isn't checked. If you move the check into repeatedly_execute_always (before frame has changed) or late_repeatedly_execute_always (after frame has changed), that should make the check happen during the animation and find your target frame. I've not tested it, but I assume that stopping a blocking animation will unblock the function and let everything continue as normal.

Alternatively, I think you'd have to move away from calling blocking animations and implement your own checks as to what is animating, which might be more complicated initially, but you know your variables will update on every engine step.

If the function that starts it is called from repexec, is that before or after the "if (Lose)" check?

That looks correct to me, so I would guess that either iLow doesn't have the value you are expecting, or your other function (that starts animating it) is re-starting it. You might want to check Object.Animating as part of the stop or start function, to make sure it's in the state that you are expecting.