RightNote has features to deal with PDFs.  From the Help file:

Indexing settings

The professional version of RightNote allows you to index attachments and links of the following file types:
.txt, .rtf, .htm/html, .doc/docx, .xls, .csv, .pdf

In the options dialog under the Indexing settings section, you can select which file types you want to be indexed by default. Further, every note has it's own setting which will override the default settings.

For example, you may want to set pdf files to not be indexed by default, since often times these can be large files, and you generally do not need the contents of these file to be indexed. If you then need a specific pdf file to be indexed, you can adjust the setting in the attachment viewer.

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Attachment note type

The attachment note type allows you to store any type of file in a RightNote database. For example you can store MS Word documents, Excel files and PDF Documents. If supported, the contents of the file will be indexed and made searchable.

Currently the following file types will be indexed:

txt, rtf, htm, html, doc, docx, xls, pdf.

You can open/view the file by clicking on the Open File link in the viewer. This will open the file with the default associated application for the file type, for example and xls file will be opened by MS Excel (if it is installed); a doc file will be opened by MS Word.

[...]
Note:

When you open an attachment, you are viewing a copy of the original document. If you make changes to the attachment, this will not affect the original source document.

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Link note type

The link note type allows you to create a link to any type of file on your computer. For example you can create links to MS Word documents, Excel files and PDF Documents. If supported, the contents of the file will be indexed and made searchable.

Currently the following file types will be indexed:

txt, rtf, htm, html, doc, docx, xls, pdf.

Note:

A link note does not store the actual contents of the file in the RightNote database. It simply points to a file on the file system (or internet url). If you open the link, you will be opening the source file pointed to by the link url.

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Warnings:
   A) I haven't tried it
   B) Features only in the Professional version, i.e. the payware one

Zombies Need Brains (ZNB) is a US small press that each year produces collections of original (no reprint) short stories from a mix of established SF&F authors and new voices found through an open submissions call. Editorial standards are rigorous, and ZNB is a SFWA-qualifying market. Each year, these books offer high-quality reading, as well as the pleasure of encountering writers new to you.  This year's Kickstarter, running until 14th September 2023, funds the following the projects:

FAMILIARS  (approx. 14 stories)
Animals have been our companions since the dawn of time, but in science fiction and fantasy, often that bond is taken one magical—or technological—step further. ...

LAST-DITCH  (approx. 14 stories)
In the heart-pounding world of espionage, it’s the spy that gets the dirty work done. ...

AMPYRIUM
Ampyrium, city of a thousand wonders! Powerful magicians called the Magnum have created a massive city contained within eight walls, each with its own portal to another world. Here, eight different magical lands collide. ...

ZNB 2023 Kickstarter
Blog post by Juliet E. McKenna (a favourite fantasy author of mine, and a contributor to ZNB anthologies)
Zombies Need Brains home page