The repository shall have a system of reliable linking/resolution services in order to find the uniquely identified object, regardless of its physical location.

This is necessary in order that actions relating to AIPs can be traced over time, over system changes, and over storage changes.

Documentation describing naming convention and physical evidence of its application (e.g., logs).

A repository needs to ensure that there is in place an accepted, standard naming convention that identifies its materials uniquely and persistently for use both in and outside the repository. The ‘visibility’ requirement here means ‘visible’ to repository managers and auditors. It does not imply that these unique identifiers need to be visible to end users or that they serve as the primary means of access to digital objects. Ideally, the unique ID lives as long as the AIP; if it does not, there must be traceability. Subsection 4.2.1 requires that the components of an AIP be suitably bound and identified for long-term management, but places no restrictions on how AIPs are identified with files. Thus, in the general case, an AIP may be distributed over many files, or a single file may contain more than one AIP. Therefore identifiers and filenames may not necessarily correspond to each other. 

APT keeps the URI of where the files are physically stored.

Naming convention used in APT: Bagging specifications#File and Directory Names

This link describes the generic file object:Member API#File Resource. Depositors can see through the web UI or Rest API where the file is stored. This URI is stored as part of the AIP. The URI does not relate to the naming convention of the files. Metadata assigned to each stored object is also an alternative way (emergency backup) to search for the physical objects. All files in preservation stored are tagged with metadata describing the name of the depositor, the name of the intellectual object/identifier, the file identifier, the file type, and SHA256 and MD5 checksum. Hence if you find that physical object, one can find where the object came from and who it belongs to. All files are self-identifying.