PDF Organization, Library?

Hello,
I have a collection of pdfs downloaded from the USPTO, specifically the Chapters from the MPEP, including a TOC pdf. It appears that the pdfs are linked, in the TOC document, there is a search link that opens up the full Acrobat search, from which all chapters in the MPEP (the collection of pdfs) can be searched. It is proving to be a great tool but I have no idea how it works, I am primarily concerned with not damaging it when I edit the individual chapters using Pro. If anyone could direct me to where I can read up on the organization or send me a note on the organization that would be great. Thanks
Further, unaware of the linkage I removed one chapter from the collection and added back another version of the same chapter which I had annotated, this chapter / pdf -the added one- is also searched when the link in the TOC is used to search.
Best,

One of the problems is the search algorithm used in the Windows search. I had searched for a file for about a year and until I found the issue with the MS search it had missed me. The search will search inside a file for only a given set of specific file types (all MS files). Other files can only be searched by name, not content. There is a flag for this in the registry. The post at http://weblogs.asp.net/owscott/archive/2008/04/04/enabling-xp-and-windows-server-2003-to-s earch-all-files-types.aspx indicates one solution.
I think this is the process that you are referring to. If not, I am sorry. It is just that MS does not tell you that they do not search the content of ALL files, only the ones they have in a list (i.e., all MS files).

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