First, many apologies for not promptly responding to your question...
I've been sick for almost two weeks, so I haven't been as active in
managing the groups as I usually am.

As noted by Shavinder, transclusions are not 'plugins'.  Transclusions
are only invoked when they are *rendered*, and thus do not get invoked
*automatically* during startup unless they are actually embedded
somewhere in your page content.  One convenient way to do this is to
add the following to your PageTemplate:

<span style='display:none' macro='tiddler SiteStartup'></span>

This will cause the [[SiteStartup]] tiddler to be rendered any time
the PageTemplate is processed.  Note the use of style='display:none'.
This allows content in SiteStartup to be handled without creating any
unintended output on the page.  Note also that, if SiteStartup does
not exist, the above span will not be rendered, so it is safe to
include this line in every document's PageTemplate, even if
SiteStartup handling is not currently needed in those documents.

Next, create your custom SiteStartup, containing any transclusions,
macros, or inline scripts that you want to invoke, like this:

<<tiddler ToggleRightSidebar>>
<<tiddler ToggleLeftSidebar>>
<<someMacro>>
<script>... JS code ...</script>
etc.

You can see an example of this technique here:
   http://www.TiddlyTools.com/#SiteStartup

> I think the documentation on TiddlyTools.com needs serious improvement.

I appreciate the feedback regarding my documentation, but I think that
the above criticism is seriously overstated.

I want my documentation to "do it's job" effectively, so that it
actually helps help people *use* the stuff I've written.  To
accomplish this, I need feedback from the community. However, rather
than merely stating that it "needs serious improvement" (which is
really just a complaint and isn't really helpful), please suggest
*specific* information that is lacking, so I can write additional
documentation that actually addresses your concerns.

I have published more than 200 addons (plugins, scripts,
transclusions, templates, stylesheets, etc.) on TiddlyTools.  Many of
these addons contain extensive documentation, and over 40 plugins have
*separate* 'pluginInfo' tiddlers because their documentation was so
extensive that people complained it bloated the plugin tiddlers
themselves.

In fact, there is about 400K of *documentation* currently contained
within over 2Mb of tiddler content.  Thus, nearly 20% of the content
of TiddlyTools is documentation, including syntax/usage instructions,
examples, configuration controls, and revision histories.

Unfortunately, despite my efforts, not all of my addons have been
documented as thoroughly as I might like.  This may be particularly so
for transclusions, as I recently re-wrote all 76 of these tiddlers to
convert from using InlineJavascriptPlugin and instead, invoke custom
JS code
using a TW-native technique based on the <<tiddler>> macro, thereby
eliminating the dependency on the plugin.

Prior to this massive re-write (which took a full week), most inline
scripts had virtually *no* documentation, except for notes embedded in
the script tiddlers' source.  As part of the re-write, I standardized
the format that I use for transclusions, and added a 'self-
documenting' mechanism so that directly viewing a transclusion tiddler
now shows *some* documentation, where previously there was none.

enjoy,
-e
Eric Shulman
TiddlyTools / ELS Design Studios
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