I agree with @Medievalist here - pick a single app. It removes a lot of the friction.
There is a huge amount of writing online on Personal Knowledge Management (PKM) which is essentially what you’re doing, but I’m guessing you don’t have time to go down that particular rabbit hole - it’s addictive reading about this stuff, but at the end of the day time spent reading about that could’ve been spent on your actual field of interest and you have to find a balance
Speaking as someone who hasn’t found that balance and loves reading about PKM, here’s what I did:
I use DevonThink Pro (DT), which is great for my use case and yours. For you, it’s got the following benefits:
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Files are stored locally on your Mac, so you do not need to worry about protected data sitting on a third party cloud service somewhere
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DT’s search function is out of this world and you will be able to find all sorts of gems in your files
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DT can handle any file type, so you can store PDFs, emails, notes you’ve made, etc. It has in-app OCR for any files that need to be turned into searchable text
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Groups and tags are your friend, and DT can also create smart groups (essentially imaginary groups based on criteria you set - great for temporary projects, etc.)
“Groups” is DT’s language for folders. For me, I have a rigid folder/group structure that separates all my files by topic. I vaguely use Johnny Decimal for my folder-naming conventions. This is top level sorting by topic because this is how I like to navigate. So for example I’m an ecologist, so my folder structure looks a bit like this (this is imaginary but based on what my actual structure looks like):
10. Conservation
10.01. Marine
10.01.01. Saltmarsh
10.01.01.01. Kelp
10.01.01.02. Sediments
10.01.02. Deep sea
10.02. Woodland
10.02.01. Trees
10.02.02. Woodland soil carbon
I have a rule that I don’t go more than 4 folders deep, and if a file fits in more than one folder it only goes as deep as I can file it. So for example if I had a paper that discussed both salt marsh and deep sea sediments, I would file it in 10.01. Marine because it cannot go any more precise.
In addition to a rigid folder structure, DT has tags. I don’t use my tags to manage topics, since I already have my file structure for that. I use tags to manage the type of file, and I have 5 bonus tags that record the action pending for a file. This is really useful though I know lots of people would be horrified at this from a knowledge management perspective. Here’s the actual list of file types I track:
(DT allows tag colours to be set, so e.g. my 5 action tags are yellow and denoted by an emoji.)
All of this combined basically means I can do things like find all my notes on talks about saltmarshes, etc.
Nowadays I pretty much file everything into my database. It has made my life so much easier. BUT. DT does have a big learning curve. It is well-worth it in my opinion, and some of the things you need to think about will have to be done for all apps and are not app-specific.
Step 1 is figuring out whether you’re a folders or tags person, and identifying how you like to navigate (do you run a search to find the file you’re after or do you prefer to navigate to a file yourself?)
Step 2 is mapping out the structure (or indeed having no structure at all - if you prefer to find files by search you don’t need folders necessarily, just pick an app with a powerful search function and let it do all the work!).
Step 3 is identifying the file types you work with. Is everything you handle in PDF, for example, or do you have a mix of different file types that need an app that handles it all? Do you have a lot of emails that ideally would also be in your library? (I’m guessing you have no weird file type that is unique to your sector, but if you do you need to think about that too. E.g. for me I have GIS files. Do I want those in the same library, and if not, where should they be stored to be easily found?)
Step 4 is figuring out what you intend to do with these files. Do you just need to be able to find things quickly? Are you planning to do research from these files? Do you want to be able to easily add notes or is it more like a library you extract data from and move elsewhere for “processing”?
Then come back here and tell us what you want to do, and we’ll recommend the app 