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Features I find useful in this context

- ace-link is great for opening visible links in a couple of keystrokes

- org-store-link for linking arbitrary places in various (possibly remote) files inside emacs

- org-agenda to generate various hierarchical/tags/other criteria views

- counsel-grep-or-swiper (with ripgrep) works well even for several years worth of notes without the need for explicit indexing

- org-attach manages attachements such as pdf files (copy/open/sync/etc) pdf-tools with a hydra enables convient reading, search of the files in emacs

- Org Babel for cleaning, querying data (among other things). Inline images work e.g., generated by emacs-jupyter

- OrgMobile for agenda views, pushing notes from mobile



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