Re: Do not see the provisioned application aspx files in “Site Content and Structure”

The trick was the “type” attribute of <File> element that provisions the aspx.

Previously I had something like:
<Module>
<File Url="PageTemplate.aspx" Name="Default.aspx" Type="Ghostable"></File>
</Module>

With this, the aspx will not appear to the browser interface. I needed to change it to Type="GhostableInLibrary".

So what are the possible values and then what the use of each?

http://msdn.microsoft.com/en-us/library/ms459213.aspx explains the attribute:
“Optional Text. Specifies that the file be cached in memory on the front-end Web server. Possible values include Ghostable and GhostableInLibrary. Both values specify that the file be cached, but GhostableInLibrary specifies that the file be cached as part of a list whose base type is Document Library.
When changes are made, for example, to the home page through the UI, only the differences from the original page definition are stored in the database, while default.aspx is cached in memory along with the schema files. The HTML page that is displayed in the browser is constructed through the combined definition resulting from the original definition cached in memory and from changes stored in the database.”

That means that you have three choices; none (you can go without specifying any value because it is optional), Ghostable or GhostableInLibrary.
And the use of each… Let me stop here for now. I have not found a document explaining it throughly, nor had time to experiment it myself.