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I use almost exclusively plain text files. If I need formatting to produce things like HTML, PDF, ... I use Markdown or LaTeX.

For images/audio, I use lossless file formats (ex: TIFF, FLAC, WAV, SVG). If I need smaller formats for a web site, for sharing or to bring it with me on my phone, I convert it to smaller formats like MP3, JPG, ... Those files are disposable when not required anymore.

During my research if I found a web page I want to refer to later on, I save it in PDF format. Why? Because PDF is fairly future-proof (ISO standard) and it's so widely used that it will not disappear anytime soon. I don't save it in HTML format because I will probably not be able to reopen it in the future because HTML spec changed too much. I don't want to have a folder full of images/css/js for each page. Also, there is no garantee I will be able to read it in the future to way I read it initially. PDF have this garantee.

For anything else (like speadsheets), I use LibreOffice the most I can. LibreOffice is based on OpenDocument open format. Open format fit in my definition of future-proof formats. And no, Microsoft OOXML format doesn't fit in my definition of future-proof format because it's driven by Microsoft (same for any big business like this). They can decide tomorrow to stop keeping the standard updated and start adding proprietary "features" in the "OOXML-NG" format (which will make Microsoft Office files unreadable in other Office suites).

For future-proof information/knowledge management, stay away from closed/proprietary softwares as much you can do.

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