Conventions on referencing manuscripts
Lemmata
Every article has a title (the lemma), and in tune with other wikis, the URL is identical with the lemma. In case of manuscripts, the lemma is composed of place name, holding institution, and shelf mark (e.g. Admont, Stiftsbibliothek, Cod. 43). Consistency in designating manuscripts is generally a good idea, as it helps find manuscripts, to check arguments, and so on; in the context of a wiki such as the Clavis wiki, uniform lemmata also help to identify doublets, to spot erroneous shelf-marks, to faciliate searches and mass edits, and to make categories easiert to navigate.
What is a manuscript, anyhow?
Every manuscript should have one and only one article. Normally, this means that every book with a shelf mark is seen as a distinct object, and hence can have its own article. Disiecta membra thus have their individual entries; e.g. St. Paul im Lavanttal, Stiftsbibliothek, 6/1 and Karlsruhe, BLB, Aug. CIII were but one manuscript in the Middle Ages but today are kept in two collections, and hence have separate articles. Vice versa, volumes composed of two or more medieval manuscripts like Arsenal 713 have only one entry. Note that libraries disagree whether multi-volume manuscripts should have one shelfmark or one for every volume, so while normally "manuscript" refers to individual volumes, occasionally it does not.
Previous collections and olim shelf-marks
References to manuscripts should always (not only in the lemma) be based on the current location of the manuscript and the current shelfmark. Previous collections and olim shelf marks can and should be mentioned in the article. In some cases, redirects are used so that users looking for manuscripts that have moved can easily find the correct article (and the current holding institution). For example, Wien, ÖNB, Cod. 16 redirects to Napoli, Biblioteca Nazionale, ex Vind. lat. 2.
Sometimes, it can be surprisingly difficult to establish what the current shelfmark is; such cases should be discussed in the respective article. Also, if a manuscript is referred to by erronous shelfmarks, this should be mentioned in more prominent cases, and if the error is wide-spread, a redirect page may be in order.
Where the current location of a manuscript is unknown, the name and shelf mark in the collection the manuscript was kept in last is used for the sake of references, and information on its current whereabouts are provided in the article. The Cheltenham manuscripts are a special case; while those today in public libraries are listed under their current shelfmarks, those in private collections are routinely cited by their Phillipps numbers, so it sometimes makes sense to list them under "Cheltenham" (e.g. Cheltenham, Phillipps Collection, 17849).
Place names
Place names are generally in the local language, which in some multi-language countries can be mildly delicate to determine. Brussels and Luxembourg are treated as francophone for the purpose of this list, so it's Bruxelles (not Brussel) and Luxembourg (not Lëtzebuerg). In almost all cases, the official names (and abbreviations) are used; the only exception from the latter rule is The Hague, which is rendered Den Haag (not 's-Gravenhage).
Names of holding institutions
For libraries and archives, the official names and abbreviations are used, which normally are in the local language. Efforts habe been taken to use the current name, so it's Archivio Apostolico (not Segreto), BnF (not BN), KBR (not Bibliothèque royale), the universities of Leiden and Gent have a universiteitsbibliotheek (but no longer are rijksuniversiteiten). French local libraries, however, are always referred to as BM whatever the current designation may be (they tend to change every now and then). In the long run, infoboxes will provide ISIL numbers for all holding institutions.
Shelf marks: spelling
For shelf marks, sometimes a frustrating variety of spellings can be observed (with or without "MS" and the like, with or without spaces, Roman vs arab numbers, capitalisation, degree of abbreviation, sometimes choice of language). Normally, we follow Kéry. If you are uncertain about the correct shelf mark, look at existing articles and/or the usage of the holding library.