File

A file is the smallest known infantry unit within the Covenant Army. Typically, files do not contain any Sangheili, unless they are exclusively Sangheili (that being there are no mixed files). A file is roughly equivalent to a UNSC fireteam or a Spartan-IV fireteam. A lance is the unit immediately superior to a file.

More Halo-aligned information at: Halopedia.

Background
Files usually contain a commander and three to four other members. Files' organisation changes depending on its role, with scouting and shocking files typically being bigger and less defined than infantry and special operations files. There is usually one file in a lance, occasionally accompanied by support.

Sangheili
A sangeili file is usually composed of three Sangheili Minors and commanded by one Sangeili Major. Sangheili files are less common than any other files and are usually used for high-priority missions. The members of a sangheili lance are handpicked by the commander, meaning that every member of a file is picked by the lance commander.

Special Operations
A special operations file is typically a group of four Special Operations Unggoy. Sometimes special operations files are made up of the Special Operations Unggoy and commanded by an Unggoy Ultra, in which case the lance commander would be a Special Operations Sangheili.

Special operations files are also sometimes made up of Sangheili, in which case it would be a group of four Special Operations Sangheili. A Special Operations Officer would never be the commander of a file, as opposed to being the commander of the lance.

Unggoy
An Unggoy file is usually commanded by an Unggoy Major and contains three Unggoy Minors. Unggoy files will usually wield plasma pistols and needlers. When wielding needlers, the commander of the file is the most likely to have the needler. Typically there are one or two needlers per file. Unggoy files are the main infantry files of the Covenant Army.

Kig-Yar
Kig-Yar files are slightly harder to define administratively. Technically, a Kig-Yar file contains four Kig-Yar Minors and is commanded by a Kig-Yar Major. The lance is also led by a Kig-Yar Major. The file structure is the same between Jackal and Skirmisher files. The main difference is that Jackal files typically work with infantry and a variety of other forces while Skirmisher files are more dependant. Because of this, Jackal lances are grouped into units commanded by Sangheili, while Skirmisher lances are grouped into units commanded by Skirmisher Champions.

Jackal files are used mainly as scouting units, often working closely with infantry and falling under the command of a Sangheili Major. Skirmishers are used as shock units, usually working fairly independantly and semi-autonomously. Skirmisher units are grouped together and led by Skirmisher Champions, which are further grouped together and commanded by a Sangheili Ultra.

Trivia

 * According to script writer Austin Rossi, unlike in a majority of Halo media, Covenant Army organization plays a significant role in the Project: Spartan-IV series novels.