Working with Folders and Sub-Folders

I'm updating this big site, and its pages are organized into
folders. I've only ever organized my images and .pdf files with
folders not my html files but all my prior sites have never had so
many files as this one. It’s starting to drive me crazy
though because pages in folders aren't connecting to scripts in the
scripts folder, menus aren't working right because of it and I'm
not sure what I can do to fix it.
My question is if images are showing up in these sub-pages,
the linked css is being applied in these sub-pages why are the
scripts not working in the sub-pages? For example, all the top
level pages easily connect to the rotating JavaScript banner, but
as soon as you go into a sub-folder page the banner disappears. All
these files are being updated via templates so any changes I'm
doing is affecting all the pages the same. That’s why
it’s confusing me why an image would connect the same but a
script wouldn't. Don't they search for their links root down or
does it search the folder its in down? How can you get templates to
work under such conditions where files are both in the root and in
folders and sub-folders?
Site reference is:
http://golfforkids.net/focus/index.html
Please note that this is a temporary domain for testing. The
top menu will pop up a window saying that it needs to be
registered. They are, just not to that domain and I don't have
access to the native domain. Sorry for the inconvenience!
Thank you for any clarification!!!

''"Are you subscribed to those subfolders?
File (Alt-F) - Subscribe"''
Please see #2 in original post:
''"2) Trying to Subscribe to folders only shows Inbox, not sub-folders for Inbox."''
Attached is an image illustrating this (this screenshot was taken after forcing Thunderbird to show Inbox folders as described in #3 of OP)
{In OP I was unable to attach images}

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I (we) can't be the only ones using sub-folders with this issue.

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Hi, I'm having a issue trying to run this script.
1.)It provides each folder with "Special" Permission over them. (Read, Write, Modify, Full control). Is there a way of making it "Full Control" Permission instead of special permission?
or
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What I tried doing in the following script is removing the inheritance of the folder then applying its level of authentication. I do get some errors and I'm pretty sure it's has to do with some files being password protected.
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$subsubfolder = Join-Path $subfolder "\*"
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The constructor you are using for the FileSystemAccessRule will only apply to the object the ACE belongs to. To have it apply to anything else, you'll have to use the constructor with the following arguments:
<Principal>, <Rights>, <InheritanceFlags>, <PropagationFlags>, <Type>
The one you're using doesn't have the flags. Those two flags enumerations control two things that you'll see in the GUI: 'Applies To' and 'Only Applies to this Object'. To have the ACE apply to the folder, subfolders and files (and have it not show as 'Special'
in the GUI), you'll want the InheritanceFlags as 'ContainerInherit, ObjectInherit' and the PropagationFlags as 'None'. Try this:
$rule = New-Object System.Security.AccessControl.FileSystemAccessRule -ArgumentList @($domainG,"FullControl", "ContainerInherit, ObjectInherit", "None", "Allow")
On a side note, check
this module out. It greatly simplifies access control. If you're interested in it and have any questions, let me know.

Working with Folders and Sub-Folders

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