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Currently, I organise my research ideas and personal notes in a series of folders, categorised by topics and subtopics, containing mostly notes (text files) and PDFs (and a few other types of files like images, videos, etc).

I recently came across personal Wiki software, which allows you to organise notes and ideas, link between them (like Wikipedia), manage files, and many many other things. I want to transform my existing structure of notes and files into a wiki one.

After doing a bit of research, I decided to try zim-wiki, which seems pretty intuitive and effective. However, I did not manage to import my current structure into the software. My files do not have a .txt extension and file names have spaces and other symbols not permitted for Windows (I use Linux, and the software seems to be tailored for Windows users). These characteristics make importing my current file structure in zim-wiki not possible. I would need to manually make all my files compliant with the Windows rules, which is a daunting task.

Thus, I am looking for a solution to my problem. Namely, I want a software that works upon my current file structure. I do not want to make changes. Ideally, the wiki has to work offline, and in Linux (I use Ubuntu 16.04).

I've seen docuwiki and mediawiki, but they seem too advanced for what I really need. It's unclear to me whether they work offline or not, and whether they can work upon my current file structure. So, i do not know whether they are useful or not. Does anyone know a wiki software that can integrate with my current file structure? Or perhaps, does anyone know how to import current file structure, with my caveats above, into zim-wiki?

PS: there are other posts asking for software recommendations (e.g.g here and here), but they are not specific to a given issue, like mine.

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    DokuWiki is a good option. It works offline and uses files instead of a database. Don’t understand how a wiki would work with an arbitrary file structure as it needs to establish its links and such.
    – Eric S
    Commented Sep 30, 2019 at 14:19
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    In case it's relevant to your concerns about file renaming, the page titles used by Zim are not identical to the file names. In particular, the ".txt" suffix on the file is not part of the page heading, and spaces in the page heading are replaced with underscores in the file name. Zim is originally a Linux application, so it supports Linux file names. Replacing spaces with underscores and adding ".txt" might be the only changes you need to make. When you're using Zim, the file name becomes pretty much irrelevant.
    – rd_nielsen
    Commented Sep 30, 2019 at 14:24

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There is a tool called jekyll, it uses the ruby ​​language, which is easy and intuitive. For the most basic use without modification, it is possible to create pages.
The files that this jekyll uses are text files in markdown language - very simple and practical that can be a simple text, this .mb file is transformed into html and css by ruby .

It is possible to host locally and in the github pages without paying anything.

With it you can create pages, stylize, add videos, files, images, links.

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    Thanks. I have used it for creating a blog, but I fail to see how it can be used as a wiki, in particular, having wiki features like linking easily from one page to the other. I would have to instead transform the whole thing into a series of html pages. But that's too much. Wiki is supposed to simplify the whole thing.
    – luchonacho
    Commented May 3, 2019 at 12:36

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