make sure all sqlite selects have indexes

Bearing in mind that these indexes are really uniqueness constraints
that just happen to also make sqlite generate indexes.

In Database.ContentIndentifier, the ContentIndentifiersKeyRemoteCidIndex
is fine as a uniqueness constraint because it contains all rows from the
table. The ContentIndentifiersCidRemoteIndex is also ok because there
can only be one key for a given (cid, uuid) combination.

In Database.Export, the new ExportTreeFileKeyIndex is the same pair as
the old ExportTreeKeyFileIndex (previously ExportTreeIndex). And
in Database.Keys.SQL, the new InodeCacheKeyIndex is the same pair as the
old KeyInodeCacheIndex.

Database/ContentIdentifier.hs

@@ -53,6 +53,8 @@ ContentIdentifiers
   remote UUID
   cid ContentIdentifier
   key Key
+  ContentIndentifiersKeyRemoteCidIndex key remote cid
+  ContentIndentifiersCidRemoteIndex cid remote
 -- The last git-annex branch tree sha that was used to update
 -- ContentIdentifiers
 AnnexBranch

Database/Export.hs

@@ -76,7 +76,8 @@ ExportedDirectory
 ExportTree
   key Key
   file SFilePath
-  ExportTreeIndex key file
+  ExportTreeKeyFileIndex key file
+  ExportTreeFileKeyIndex file key
 -- The tree stored in ExportTree
 ExportTreeCurrent
   tree SSha
@@ -165,9 +166,6 @@ getExportTree (ExportHandle h _) k = H.queryDbQueue h $ do
 	return $ map (mkExportLocation . fromSFilePath . exportTreeFile . entityVal) l
 
 {- Get keys that might be currently exported to a location.
- -
- - Note that the database does not currently have an index to make this
- - fast.
  -
  - Note that this does not see recently queued changes.
  -}

Database/Fsck.hs

@@ -40,7 +40,7 @@ data FsckHandle = FsckHandle H.DbQueue UUID
 share [mkPersist sqlSettings, mkMigrate "migrateFsck"] [persistLowerCase|
 Fscked
   key Key
-  UniqueKey key
+  FsckedKeyIndex key
 |]
 
 {- The database is removed when starting a new incremental fsck pass.

Database/Keys/SQL.hs

@@ -52,6 +52,7 @@ Content
   key Key
   inodecache InodeCache
   KeyInodeCacheIndex key inodecache
+  InodeCacheKeyIndex inodecache key
 |]
 
 containedTable :: TableName

doc/todo/sqlite_database_improvements.mdwn

@@ -2,24 +2,14 @@ Collection of non-ideal things about git-annex's use of sqlite databases.
 Would be good to improve these sometime, but it would need a migration
 process.
 
-* Database.Keys.SQL.isInodeKnown seems likely to get very slow
-  when there are a lot of unlocked annexed files. It needs
-  an index in the database, eg "InodeIndex cache"
-
-  It also has to do some really ugly SQL LIKE queries. Probably an index
-  would not speed them up. They're only needed when git-annex detects
-  inodes are not stable, eg on fat or probably windows. A better database
+* Database.Keys.SQL.isInodeKnown has some really ugly SQL LIKE queries. 
+  Probably an index would not speed them up. They're only needed when
+  git-annex detects inodes are not stable, eg on fat or probably windows.
+  A better database
   schema should be able to eliminate the need for those LIKE queries.
   Eg, store the size and allowable mtimes in a separate table that is
   queried when necessary.
 
-* Database.Export.getExportedKey would be faster if there was an index
-  in the database, eg "ExportedIndex file key". This only affects
-  the speed of `git annex export`, which is probably swamped by the actual
-  upload of the data to the remote.
-
-* There may be other selects elsewhere that are not indexed.
-
 * Database.Types has some suboptimal encodings for Key and InodeCache.
   They are both slow due to being implemented using String
   (which may be fixable w/o changing the DB schema),