Add a `Dirty` boolean to the `ContainerBase` class. This will be set to
true when the container mutates itself (e.g. remove, mergeBack, clear).
The dirty bit is reset when running `PipelineManager.store`.
Drop using the `revng-` prefix from all executables under
`libexec/revng/`. Now any executable found under there that is
executable and without extension will be considered a `revng`
subcommand, following the usual command-line rules.
Replace the stub implementation of invalidation with the proper
implementation. A ReadPathCache is added to each global so that it can
keep tracks of what target are associated to which read paths.
Giacomo Vercesi