Clooz by Ancestor Detective may be what you are looking for. Clooz might eventually take the place of your research notebooks. And you would not have to do it all at once but start using Clooz for future research at the same time you are linking material from the notebooks to individuals.
From the Clooz manual, page 8,"The goal of Clooz is to help you organize all the tidbits of information you gather...Many of us [consign these bits] to obscurity in our 'filing' systems."
One of the first things to do after installing Clooz is to let Clooz import your project individual names and numbers into Clooz. You can add new individuals as you discover them, or delete individuals.
Clooz creates several kinds of reports. Not the reports you would put in a book or share with others but searchable research reports to help you organize what you have found as in a group of people with a common event. or all events and sources connected to one person. And this material is searchable.
I quote from page 10 of the documentation for Clooz v. 1.1.
This program uses easy templates for Censuses, Documents, Directories, Photos, and Sources. Just about anything else could fit into the Source template.
I purchased Clooz hoping it would help me record sources that I had searched and list the individuals who I had NOT found, thus providing a list of sources to NOT look at again and again for those individuals.
However, Clooz does NOT record that type of negative search. That is, it can but not easily.
The 1998 URL for this program is/was http://www.ancestordetective.com.
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