C-Command Software Forum

How do you use EagleFiler?

I am looking around for different kinds of get-organized, PIM-like, GTD-ish, keep-track-of-data, list-making, calendaring software, and have come across Eagle Filer for the first time.

I have to say that I’m a bit confused about the value Eagle brings. Take OnmiFocus: its (ahem) focus is to-do’s. Circus Ponies’ Notebook has that really great Multidex, and bunches of annotation tools.

But Eagle seems to be a program that just manipulates folders and files.

What am I missing? How do you folks use Eagle? what do you find compelling about it?

Thanks for enlightening me!

File organization
I chose EagleFiler for two reasons: 1) Tags and 2) My files are not moved, renamed, encoded, or locked into a proprietary database format.

To organize my files, I use several EagleFiler libraries: CommerceArchive, DeveloperArchive, SoftwareArchive, ReferenceArchive, and ResearchArchive.

Obviously my classifications make sense to me, but to give you an idea, I keep all of my PDF receipts, order confirmations, and statements in the Commerce library. I maintain a minimum sub-folder hierarchy and rely on descriptive tags for organization. Now, I can quickly search to find the PDF of my last utility statement, and if I need to email it, I do not have to export the file from a proprietary database instead I just navigate through the Finder and attach it to the email.

The other libraries are used in a similar fashion. If I need to remember how to codesign the new version of DavMail then I just open my Developer library and search for codesign – simple.

My Software library is by far the largest in memory size because I store disk images (dmg, iso, exe) along with license files, instructions, and user manuals. Right now this library is over 16GB, and it opens in about 2 seconds if EagleFiler is already running.

For my Reference library, I combine EagleFiler with BibDesk. In this case, I am really only using EagleFiler to “hold” my PDF journal articles and PDF textbooks, but what I like about this setup is that BibDesk will maintain a link to the PDF even if I use EagleFiler to move the file into a sub-folder.

So to summarize, I use EagleFiler as an extension of the Finder and Spotlight (really the question that you were asking). Without EagleFiler, I would be using a much more extensive sub-folder organization system, and I do not want to go back to the bad old days of having dozens of nested folders . . . (essentially the additional layers of folders are needed to replace the tags, but with smart folders, I can have files grouped together that would never be filed in the same subfolder)

What else? I do not use Dropbox. Instead I use Synk Pro 7 from decimus.net for synchronizing libraries across machines. I have Circus Ponies’ Notebook and Aquaminds Notetaker – don’t use them. I tried Together, Devonthink, Tagit, Leap – didn’t like them (personal taste). Tried Microsoft OneNote using Windows 7 and VMWare Fusion – good program but not for organizing files.

I did try using EagleFiler for email archiving, but because I use multiple machines plus an iPhone and now an iPad, I decided to setup my own IMAP server instead (Works great with MailTags).

I also like the fact that the developer, Michael Tsai, is always responsive to requests in the user forum.

Gook luck . . .

I moved over to EagleFiler from the now defunct Journler.

Like junkmail, I have a library for keeping track of purchases and financial matters. I call it Web Receipts. I can store pdf receipts, confirmation and shipping-emails, bank statements, etc. all in Eagle Filer, and (if I tag consistently) find things quickly and easily.

I have another library called Meetings that I use for organizing files and notes for various meetings I attend.

I’ve not looked at Circus Ponies, so I can’t offer a comparison there.

I think I will chip in as a grad student. I use EagleFiler to manage all my school related materials. I have a library for each semester so that I can review what is going on, all at once. I put them all in Dropbox and I have never had a problem so far. I am not good at organizing stuff but EagleFiler helps me to discipline myself better.

Some examples:
-I do not have to open another application or multiple windows to check my syllabi.
-I can easily find my writings, all in one window.
-Sometimes, I need to pull out my paper at school; then I just log onto Dropbox.

  • *Update: I directly write within EagleFiler when it comes to a simple draft.

Now that I can import PDFs more freely, I am looking into a possibility to manage references. Finally, support from the developer is hard to beat; it really makes me comfortable/confident in continuously using Eaglefiler.


@Junkmail–It is helpful to read how you use Eaglefiler. About managing references, could you elaborate it a bit more, please? My struggle is to maintain citations along with actual articles. I have tried Mendeley but Mendeley keeps duplicating files. I would really appreciate any input from you.



This is my reference collecting workflow (given for journal articles - other searches are similar); it may be long and repetitive.

  1. Search for scientific journal articles using SciFinder, Web of Science, Google Scholar, etc.

  2. Download, rename (full title of the journal article), and save as PDF to EagleFiler.

In my ReferenceArchive library, I created a minimum folder structure to facilitate accessing files from outside of EagleFiler (Articles, BookChapters, Books, ConferenceProceedings, JournalArticles, Magazines, Patents, Presentations, References, TechnicalReports, Theses, and UserManuals). I save files (PDF, Word, Text, Excel) directly to the relevant folder and then use the “Scan for new files” command to add them to the library. I might also have to apply the “file name to title” script.

  1. Assign tags to documents in EagleFiler

I assign a tag to each document that is the same as the storage folder (articles, book_chapters, books, conference_proceedings, journal_articles, magazines, patents, presentations, references, technical_reports, theses, and user_manuals). This is to facilitate smart folder searches. For books and patents, I also assign relevant tags for content (engineering, civil, chemical, electrical, mechanical, instrumentation, software, mathematics, etc.).

  1. Download and import citation + abstract in BibTex or plain text format to BibDesk

I use SciFinder, Web of Science, etc. to download citation + abstract in BibTex format (or plain text format). When connected to my University network, I use a Web of Science search directly in BibDesk.

I import the reference to BibDesk. I then use a top (BibDesk) bottom (EagleFiler) split/divided screen orientation. With the new import selected in BibDesk, I drag the document from EagleFiler up to the BibDesk sidebar. This creates an alias in BibDesk.

  1. Assign “BibDesk” tag to document in EagleFiler

I go back and add an additional tag to the document so that I keep track of the EagleFiler documents that have a bibliographic entry in BibDesk.

  1. If the keywords did not import to BibDesk, I will copy and paste them from the document in EagleFiler or create them based on the document title.

To summarize, I use two applications to manage my references. EagleFiler to “hold” the documents and BibDesk to organize citations.

I maintain only one EagleFiler library and one BibDesk bibliography for all of my references (1000+ documents and counting). For individual projects, I will create temporary BibDesk bibliographies to hold relevant citations (easy since they are really only text documents).

I assign keywords only in BibDesk and use limited broad tags in EagleFiler. This is to keep from duplicating function and also to limit tag “clutter” in EagleFiler.

When I start a new project, I will search BibDesk by keyword and then open documents by double-clicking the included link. At this point, the only reason that I would open EagleFiler is if I think that I forgot to import a document to BibDesk.

To get the citations into a manuscript, I use Microsoft Word 2011 and BibDesk to Word. That website has not been updated in awhile, but the latest version does work with Word 2011.

Other thoughts?

I tried to force myself to use Sente because they came out with a great looking iPad app, but I just did not like the Mac application . . .

Instead, I use PDF Expert (or ReaddleDocs) with a Synk Pro script to synchronize my Books and JournalArticle folders in EagleFiler (occasionally I run the “Update Checksome” command) to my iPad. I like PDF Expert because my highlights and notes are viewable and can be edited back in Acrobat or Preview.

It would be nice to get searchable abstracts from BibDesk to the iPad, but I haven’t tackled that one yet . . . maybe I will join the BibDesk development community and write an iPad app . . . in my spare time . . . yeah . . . spare time . . . as a doctoral candidate . . .

@Junkmail–Thank you a lot. It really helps me to think through how I should organize my workflow. I also realize that I should do some work at the time that I import articles, like reviewing citations or making corrections, not later. It is great to know that I can make aliases just by dragging files from Eaglefiler.

Best wishes,

I use Eaglefiler in two distinct, if related ways. I won’t go into the same useful detail as above, but just give you a hint of how it helps me.

1.) Blogging. I have to read tons of rss feeds, blogs, and websites looking for items. Eaglefiler lets me snip and organize everything as I go. (I save them as pdf’s so they are accessible on my Windows laptop, but webarchives are even better.) This info. would easily becoming overwhelming if I did not have such a useful way to organize clippings. I can throw pdf papers and word documents in as well, as needed, and create text files for ideas that occur to me on the fly.

2.) Big projects. This is why I bought it. On my large research projects, I found myself drowning in paper and disorganization. I still do print out quite a lot of stuff, but Eaglefiler ensures that the electronic versions of everything I need are in one place, easily searchable. (Brilliant when it comes to fact-checking.) I also print out less than I use to, using Skim or PDFPen in tandem with Eaglefiler. I’m a folders person, not a tags person, so I’ll have a folder for–say–interview transcripts, emails, cvs, research papers, news clippings, and so on.

Though I said I use it for two things, I was thinking professionally: I also now use Eaglefiler to keep track of everything in my personal life. Record reviews get snipped, school emails go into a file, web pages from Xmas shopping. And on and on.

I’ve got my live libraries on Dropbox, and all files are accessible from my Windows laptop. Eaglefiler is so handy that I regret having to fire up the PC, though.

PS I realize I didn’t mention how I use libraries: One main one for blogging, small work projects, and all personal stuff. One for each large project (which I stop using once the project is done). One mail archive and one general archive–where I send obsolete source material from my first, main library.

junkmail- I’m curious about how you use Synk Pro to sync with PDF Expert. Could you give some more details about how to set this up? Your excellent post helped prompt me to give up on Sente and its clunkiness and switch to Eaglefiler and PDF Expert.