How I Organize my File System

A friend purchased a new computer. He asked me how to move away from keeping many of his documents on the desktop. I recommended that he start with what I do and then adapt that to his needs.

This note describes how my file system is organized. I’ll start by explaining the five key folders and what they hold. Then I’ll look at the naming rules I follow for the files. A lot of detail has been give, so I summarize the file-naming practices and my key workflows. A brief look at the literature that has inspired by system follows. Finally, I’ll suggest next steps for those who want to use my system as a starting point.

THE KEY FOLDERS

All my documents are kept in five top-level folders in a cloud storage system. My cloud system is iCloud but it used to be Dropbox. I switched primarily because Obsidian, the app I use for note taking, is designed to sync with iCloud but not with Dropbox.

I use five folders keep all my documents. See this illustration.

I Use Five Top-Level Folders

You can see that I prefix the names of the folders with a digit and a space so that the MacOS Finder displays them first.

The folder “0 inbox” serves two purposes. It is the downloads folder for all the web browsers. It is also a scratch area where files go temporarily. For example, if I create a document in an application, I often save it to the “0 inbox” folder and then move it to its permanent location.

The folder “1 active-topics” contains only other folders at its top level. There is one folder for each topic I am actively working on. The topics correspond to Taigo Forte’s (2022, Chapter 5) areas of responsibility and to his resources for topics of interest. Each topic has a two- or three-position code that I write in all caps. Once I assign a code, I don’t change it. Later I will give some examples and explain how each of the topic folders is organized.

The folder “2 inactive-topics” is where topic folders are moved when I am no longer working on the topic. When the cloud file system fills up, I move folders for inactive-topics to an external disk drive that has the name “archive”.

The folder “3 works” is where I store documents that others have created. As I’ll describe in more detail later, it is mostly files but does have a few folders.

The folder “4 notes” contains all my notes. It is structured as a Zettelkasten and will be described later.

NAMING RULES FOR FILES AND OTHER FOLDERS

Inside the top-level folders, are other folders and files. This section describes the rules I use to name them.

The inbox Folder

Many of the files in the “0 inbox” folder are documents created by others.

These and other documents are named so that their name conforms to the pattern “{creator}-{date}-{title}{extra}.{extension}”.

• The {creator} field is the name of the author when that is known, otherwise its the name of the publishing organization. For example, for a publication by John Smith published by IBM on their website, the {creator} is “SmithJohn” — last name followed by first name. If the author had not been given, the creator would be “IBM”.
• The {date} field is either the exact date or the year. An exact date is written like “20240125” when means January 25, 2024. Dates written like this will be sorted by the MacOS Finder into date-created order. When documents don’t have a date, I leave the field empty, writing, for example “SmithJohn--the best yogurt ever.pdf”. That potentially makes searching for documents easier, as there always is a date field, even if sometimes it is empty. I don’t write out dates with dashes as in 2024–01–25 so that the date field is always between two dashes, something that helps if I want to process the file system with a computer program.
• The {title} field hold the title of the work, except that I leave out characters that my file system does not support. Unfortunately, the colon character (“:”) is used frequently in titles but isn’t accepted by the MacOS Finder. When the book title has a colon, sometimes I leave it out of the file name and sometimes I replace it with a hyphen.
• The {extra} field is optional and is used to hold information that helps me identify the document if I need to enter its bibiographic information into my bibliography manager which is Zotero. Usually it is omitted. For example, if the document is a Tweet, I write something like “SmithJohn-20240125-the best yogurt ever (Twitter).pdf”. In Zotero, I will create a blog-post entry for this document. I don’t create the Zotero entries until and if I need them for a publication I write.

Documents that I create are named the same way, except I am the author. So my document names start “LowranceRoy-”.

The “0 inbox” sometimes contains folders. These are named in ad hoc ways.

The active-topics Folder

As explained earlier, the “1 active-topics” folder contains only folders at its top level. The names are in the form “{topic-code} {name of topic}”, where the {topic-code} is two or three upper-case characters.

Inside each of these topic folders is a list of folders, one for each project or subtopic. A project here may be a multi-step set of related tasks. It may or may not have a deliverable which causes the project to finish.

The name of a project or subtopic folder is in the pattern “{topic-code}{sequence-number} {project or topic name}” as illustrated below.

Expanded CHS Topic Folder

When I start a new project, I increment the previous sequence number and give the project a name. That was the practice at consulting firms where I worked: the client was identified by a short code, the project was identified by the client code followed by an increasing sequence number.

Usually I start the project sequence numbers with two digits, but if I anticipate many projects for a topic, I start with three digits. I have converted two digit codes to three digit codes when that was necessary.

The structure of a project or topic folder depends on the kind of project or topic. For projects in which I am creating output, I often start with these subfolders:

• input. This folder holds aliases to documents that others have created, with the original document being in the “3 works” folder. Some projects have documents that are stored only in the project folder. These are documents that I am pretty sure would not be useful outside of the project. An example might be correspondence about the project. When a project finishes, I often review the input folder and see what documents are of more general usefulness and move those to “3 works” and create an alias.
• output. This folder holds documents that I have sent to others. It has a subfolders with a name in the pattern “{date} {person or organization}”. Having a copy of everything that I have sent has proven to be useful many times.
• work. My own work is in this folder. If I share my work, a copy is created and put into the output folder.

The inactive-topics Folder

The inactive-topics folder holds a long sequence of folders, one per topic that I am no longer working on.

The works Folder

The works folder holds documents created by others and final versions of my own works. The file names follow the pattern described above, name “{creator}-{date}-{title}{extra}.{extension}”.

Sometime the work does not fit into a single document. When that happens, I create a folder with the same name pattern and put the constituents documents into it.

This folder has many files. My cloud storage system detects files that have not be used in a while, and replaces those files with links to the actual file which is then stored only in the cloud, saving space on my hard disk.

The notes Folder

The notes folder holds all my notes for all the topics of interest. It is very long.

The software I use for note creation is Obsidian. The structure of the notes is a Zettelkasten, which means that notes refer to other notes through links in the notes. A Zettelkasten also has an associated workflow.

My workflow is based on how Niklas Luhmann used his Zettelkasten, which is described by the Niklas Luhmann Archive (2024). The major steps in the workflow are to read a work by someone else and create a “literature note” on that work and then to review that literature note to create or modify “permanent” notes.

In my system, a literature note has the same file name as the underlying document. The suffix is usually different, because Obsidian files have a “.md” suffix since they are plain text files encoded using Markdown and the source document for the work is usually kept in the creator’s orignal file type, which is often “pdf” or “xdoc”. The folder is different — source documents are in “3 works” and my notes are in “4 notes”.

The permanent notes have names that reflect the my own insights. They contains links back to any literature notes. They also contain links to other permanent notes. In Obsidian, a link denoted by writing a file name in double square brackets, like this: “[[CMP07 camping in cold weather]]”. In Obsidian, you omit the file extension when writing a link.

In addition to the literature and permanent notes, I create a file in the notes folder for each topic. For example, there is a file “CMP camping.md”. There is also a file for each project or topic for which I have notes. The file “CMP07 camping in cold weather.md” was created when I wrote my first note about the topic.

SUMMARIES OF KEY PRACTICES

Summary of file and folder naming conventions

Here is a summary of my naming conventions:

• {creator}-{date}-{title}{extra}.{extension}: A file holding a work.
• {creator}-{date}-{title}{extra}.md: A file in my Obsidian vault holding my literature note on the work. The related file holding the work itself has the same base file name. The Obsidian user interface hides the “.md” extensions, but you can see it in the Finder.
• {topic code} {topic description}: A folder for a topic. Topic codes are always written in all caps. They have two or three positions.
• {topic code} {topic description}.md: A file in my Obsidian vault for the topic. Literature and permanent notes link to these files.
• {topic}{sequence number} {description}: A folder for a project or a subtopic. These folders are in a topic folder.
• {topic} {sequence number} {description}.md:A file in my Obsidian vault. Literature and permanent notes link to these files. If the file is for a project, my notes on the project are in the file. Typically I will write down the goal for the project and keep a log of the major events for the project.
• input, output, work: Folder names in project folders for projects in which I create some work, holding respectively, works from others, output that I have sent to others, and my own work.
• {a descriptive name}.md: A folder in my Obsidian vault that contains a permanent node. The description doesn’t look like a literature note file name, so that I can easily distinguish the notes.

Summary of main workflow practices

When I read a work by someone else and decided to take notes on it, I write a literature note. It has page numbers if the work is paginated, section names if the work is not paginated, and time codes if the work is a video. The notes are sometimes quotes for the source work and sometimes my paraphrases of the text. Usually I decided to write the literature note because the work has inspired my own thoughts. Those thoughts go into permanent notes. The permanent notes link by to the literature note and to other permanent notes. The literature notes link to permanent notes that use their content. The permanent notes are written as if for publication, which means that they use in-line citations for works by others.

When I start a project, I create a folder for it in the most-relevant active topic folder. Then I create a file in my notes with the same name as the notes folder. If the project is complex, I build out the note folder for it to include the project goal, team members, and start a log of the major events for the project.

PRACTICES OF OTHERS

My system was designed after using a few other systems, most notable, ones from Forte, morganeau, and Noble.

Forte’s PARA System

A recent popular method for organizing files is called “PARA”. It is described by Tiago Forte (2022, Chapter 5). Each letter stands for a high-level folder: Projects, Areas, Resources, and Archive. The Projects folder contains a folder for each active project. In Forte’s system, a project has a defined ending event such as the delivery of a software project. Areas holds folders related to one’s areas of responsibility, such as personal financial management. The areas don’t necessarily have ending events and can run for years. The Resources folder contains a folder for each of your interests. The Archive folder holds inactive projects, areas of responsibility, and interests.

In Forte’s workflow, a project folder, responsibility folder, or interest folder contains all the related file — works from others and your own works. Notes are kept in the storage system managed by a note-taking application. Those notes are structured using the same PARA organization. When a new project is started, a folder for it is created in the file system and note-taking app. Then relevant material from other parts of the filing system are copied or aliased into the new project folder.

My system differs in that I blend together projects, responsibilities, and interests into just topics. That avoids a level of folder nesting in my system. Also, rather than put projects into a Projects folder, I put them into the most closely related topics folder. All my notes are in my notes folder, as in Forte’s system. Usually works from others go into my top-level works folder.

Another difference is that my archive is on an external disk drive that is backed up offsite.

Morganeau’s Obsidian-based Zettelkasten

Morganeau, a YouTube presenter, says in her 2023 video “Note Naming in a Zettelkasten” that she uses hyphens instead of spaces in her note file names. She does that in order to make it easier to access files in a terminal session and because it looks good to her. I tried her approach for a while, but found that it made putting the entire document title in the file name more difficult, so I stopped. Now my document files in both my notes and works folders have spaces in their file names. Putting the entire original work title in the note and document makes it easier to find documents again when I need to create a bibliography entry in Zotero. If an abbreviation for the file name is used, then bibliography entries may need to be created when the original work is processed and that would be an extra step in my workflow.

Morganeau separates the last name and first name of the creator with a dash. I don’t do that. Instead I use camelCase. Morganeua would use “Smith-John-{date}-each-word-in-the-title.md” and I would use “SmithJohn-{date}-each word in the title.md”.

Noble’s Project Folder Structure

In 2009, William Noble described how to organize a project folder for computational biology projects. This structure is a good starting point for organizing the work folder when you have a project that revolves around analyzing data.

I use a variant when a project involves coding.

SUGGESTIONS FOR GETTING STARTED

To get started

• Create the top-level folders in your cloud system: inbox, active topics, inactive topics, works, and notes.
• Reconfigure your web browsers to put their downloads into the inbox folder.
• Take all of your existing files and put them into the inactive topics folder.

Now you have started. As you work, identify the topics that matter to you and create topic folders for them. Likewise for projects that you work on. Move folders and files out of the inactive folder to get started.

Expect the best structure for you to evolve over time. Hence, don’t try to get everything super well structured at first. Fix the structure as you go.

In my friend’s approach, his recently used file and folders are on his desktop. In my system, these are in the top-level active-topics folder. In MacOS, the Finder has a Recents folder that holds the most recently-used files. You can locate the folder in the left sidebar of the Finder window. I create an additional Finder folder that I call Recent Folders. How to do that is described in the Apple support community at https://discussions.apple.com/thread/252596700?sortBy=best.

WORKS CITED

Forte, Tiago. Building A Second Brain. Simon & Schuster, 2022.

morganeau. Note Naming in a Zettelkastern (Physical and Digital). https://www.youtube.com/watch?v=FkB5FmgUY1I. Accessed 26 Jan. 2024.

“Niklas Lumann-Archiv.” Der Zettelkasten Niklas Lumanns, https://niklas-luhmann-archiv.de/nachlass/zettelkasten. Original in German; I read a translation to English generated by Google Chrome. Accessed 19 Jan. 2024.

Noble, William Stafford. “A Quick Guide to Organizing Computational Biology Projects.” PLOS Computational Biology, vol. 5, no. 7, July 2009, p. e1000424. PLoS Journals, https://doi.org/10.1371/journal.pcbi.1000424.

Shortcut to Display Finder “recent Folder… — Apple Community. https://discussions.apple.com/thread/252596700?sortBy=best. Accessed 30 Jan. 2024.