except for graph-parser and publish deps
- Removed most mentions of 'repo' in deps, which cleaned up a lot related
to export cli and worker
- Removed db-based-graph? checks in deps except for unknown use
in entity-plus?
- Removing db-based-graph? checks resulted in deleting unused file graph
code paths e.g. get-pid
- Removed file graph handling in cli list command
- Remove file-based-graph? checks from deps
Improves :errors of invalid errors to be more user friendly.
Also enable closed-value validation optionally as it is useful
to have higher data quality for non RTC graphs
Introduced a breaking change for query and search commands where
graph(s) are specified as options instead of arguments. This
makes local graph usage consistent across all commands.
Also fixed in-app search not working and local query with multiple
graphs not querying from the right db
Also update export-edn command to have same default behavior as
export command. Printing to stdout was ok for dev but is surprising and
possibly overwhelming for most graphs
