Fossil is designed with features to give it a high level of integrity so that users can have confidence that content will never be mangled or lost by Fossil. This note describes the defensive measures that Fossil uses to help prevent information loss due to bugs.
Fossil has been hosting itself and many other projects for years now. Many bugs have been encountered. But, thanks in large part to the defensive measures described here, no data has been lost. The integrity checks are doing their job well.
The Fossil repository is stored in an SQLite database file. (Addition information about the repository file format.) SQLite is very mature and stable and has been in wide-spread use for many years, so we are confident it will not cause repository corruption. SQLite databases do not corrupt even if a program or system crash or power failure occurs in the middle of the update. If some kind of crash does occur in the middle of a change, then all the changes are rolled back the next time that the database is accessed.
A check-in operation in Fossil makes many changes to the repository database. But all these changes happen within a single transaction. If something goes wrong in the middle of the commit, even if that something is a power failure or OS crash, then the transaction is rolled back and the database is unchanged.
The content files that comprise the global state of a Fossil repository are stored in the repository as a tree. The leaves of the tree are stored as zlib-compressed BLOBs. Interior nodes are deltas from their descendants. A lot of encoding is going on. There is zlib-compression which is relatively well-tested but still might cause corruption if used improperly. And there is the relatively new delta-encoding mechanism designed expressly for Fossil. We want to make sure that bugs in these encoding mechanisms do not lead to loss of data.
To increase our confidence that everything in the repository is recoverable, Fossil makes sure it can extract an exact replica of every content file that it changes just prior to transaction commit. So during the course of check-in (or other repository operation) many different files in the repository might be modified. Some files are simply compressed. Other files are delta encoded and then compressed. While all this is going on, Fossil makes a record of every file and the SHA1 or SHA3-256 hash of the original content of that file. Then just before transaction commit, Fossil re-extracts the original content of all files that were written, recomputes the hash, and verifies that the recomputed hash still matches. If anything does not match up, an error message is printed and the transaction rolls back.
So, in other words, Fossil always checks to make sure it can re-extract a file before it commits a change to that file. Hence bugs in Fossil are unlikely to corrupt the repository in a way that prevents us from extracting historical versions of files.
Manifest artifacts that define a check-in have two fields (the R-card and Z-card) that record MD5 hashes of the manifest itself and of all other files in the manifest. Prior to any check-in commit, these checksums are verified to ensure that the check-in agrees exactly with what is on disk. Similarly, the repository checksum is verified after a checkout to make sure that the entire repository was checked out correctly. Note that these added checks use a different hash algorithm (MD5) in order to avoid common-mode failures in the hash algorithm implementation.
Every structural artifact in a Fossil repository contains a "Z-card" bearing an MD5 checksum over the rest of the artifact. Any mismatch causes the structural artifact to be ignored.
The file delta format includes a 32-bit checksum of the target file. Whenever a file is reconstructed from a delta, that checksum is verified to make sure the reconstruction was done correctly.
Some version control systems make a big deal out of being "high performance" or the "fastest version control system". Fossil makes no such claims and has no such ambition. Indeed, profiling indicates that Fossil bears a substantial performance cost for doing all of the checksumming and verification outlined above. Fossil takes the philosophy of the tortoise: reliability is more important than raw speed. The developers of Fossil see no merit in getting the wrong answer quickly.
Fossil may not be the fastest versioning system, but it is fast enough. Fossil runs quickly enough to stay out of the developer's way. Most operations complete in milliseconds, faster than you can press the "Enter" key.