Here we describe what each of the primary folders present in a Clay desk. This organization is merely a convention, and the exact location of any file does not affect its operation. That being said, some Ford runes are designed with this structure in mind, and applications such as dojo and spider look in specific folders for code to run. Furthermore, this organization is not perfectly adhered to - sometimes you may find structure definitions in /lib, for example.

• /app contains userspace applications, i.e. Gall agents.
• /gen contains generators. Many applications make use of generators, but also each generator in this folder may be run from dojo using +. For example, /gen/foo/hoon in the %base desk is run with +foo. Generators on desks other than %base can be run with +desk!generator like +garden!foo.
• /lib contains libraries that may be shared by multiple agents, threads, generators, etc. However, this is not the location of the standard libraries (see /sys). Libraries are imported from /lib with /+.
• /mar contains mark definitions.
• /sur contains shared structure definitions. Whenever you expect structures to be used by code across multiple files, it is recommended to place their shared structures in /sur. Structures are imported from /sur with /-.
• /sys contains the code that defines the kernel and standard libraries. Note that only the %base desk should contain these /sys files, other desks omit the directory and instead just depend on %base. /sys/vane contains the code for the vanes, aka kernel modules. /sys is the exception to the rule - structures and functions that are central to Hoon, Arvo, and its vanes, are all located within this folder rather than in /lib and /sur. See below for more information on /sys.
• /ted contains threads. These may be run from dojo using -. For example, /ted/foo/hoon on the %base desk is run with -foo. Threads on desks other than the %base desk can be run with -desk!thread like -garden!foo.
• /tests contains unit tests intended to be run using the test thread. To run a particular test +test-bar in /tests/foo.hoon in dojo, enter -test %/tests/foo/test-bar ~. If a file is specified, every test in that file will run. If a folder is specified, every test in that folder will run.

/sys

/sys contains four files: hoon.hoon, arvo.hoon, lull.hoon, and zuse.hoon. These are the files used to construct kernelspace. Only the %base desk contains these files, other desks omit the /sys directory and instead just depend on %base. The chain of dependencies is hoon.hoon -> arvo.hoon -> lull.hoon -> zuse.hoon. We give a brief description of each of them.

• hoon.hoon contains the Hoon compiler and the Hoon standard library. The Hoon compiler is self-hosted. This is the first file loaded by the Nock virtual machine, Vere, in order for it to learn how to interpret Hoon. The kelvin version number is the subject of hoon.hoon, currently at 140. One may see this from dojo by inspecting the subject with . and noting that %140 is the final entry of the subject.
• arvo.hoon contains the Arvo kernel and additional structures and functions directly relevant to the kernel. This is Urbit's "traffic cop", and as such contains the structure definitions for call stacks such as ducts and bones. Once Vere understands Hoon, it loads and interprets arvo.hoon to create the kernel. hoon.hoon is the subject of arvo.hoon.
• lull.hoon primarily contains structures shared among the kernel and its vanes, as well as a few functions. In particular, this includes the definitions of the tasks and gifts utilized by each vane, each of which are documented in their respective documentation. lull.hoon is loaded by the kernel during the larval stage in order to prepare to create the vanes. arvo.hoon is the subject of lull.hoon.
• zuse.hoon is the Arvo standard library. It consists primarily of functions shared by the kernel and vanes, such as the ones related to cryptography. zuse.hoon is loaded by the larval kernel following lull.hoon. lull.hoon is the subject of zuse.hoon. Then zuse is the subject of the vanes. Some of the functions in Zuse are documented here.

Desks

A desk is an independently revision-controlled branch of a ship that uses the Clay filesystem. Each desk contains its own apps, mark definitions, files, and so forth. The basic filesystem structure is the same for all desks, with the exception that only the %base desk contains a /sys directory. Additionally, there are a handful of special files related to the management of desks and their Gall agents:

• sys.kelvin - This specifies the version of Arvo the desk is compatible with. This file is mandatory in all desks.
• desk.bill - This file specifies the Gall agents on a desk which should be automatically started when it's installed. This file may be omitted if there are no agents to start.
• desk.docket-0 - This file configures the tile, glob and other metadata for apps with a front-end. This file may be omitted if the desk does not have a tile or front-end to be installed. This file is versioned so the number appended may change in the future as changes to its specification are made. See the Docket File documentation for more details.
• desk.ship - This specifies the original publisher of the desk and is useful if a desk is being republished. It is optional and may be omitted.

For more details of creating and distributing desks, see the Software Distribution documentation.