Add heal parsers (#97)

* annotator modules added by passing config val

* fix merge conflict

* following same pattern as parsers , modify configs

* fix to dug config method

* fix old dug pipeline for backward compatiblity

* correct default annotator type

* reflective changes

* typo extra quotes

* annotator type not being picked up from config

* remove annotate simple , log env value for lakefs enabled

* testing lakefs off

* add more logging

* add more logging

* post init for config to parse to boolean

* put back task calls

* revert some changes

* adding new pipeline

* lakefs io support for merge task

* fix name

* add io params for kg tasks

* wire up i/o paths for merge

* fix variable name

* print files

* few debug logs

* few debug logs

* treat path as path not str

* few debug logs

* some fixes

* logging edge files

* bug fix knowledge has edge

* re-org graph structure

* adding pathing for other tasks

* pagenation logic fix for avalon

* update lakefs client code

* fix glob for get kgx files

* fix up get merged objects

* send down fake commit id for metadata

* working on edges schema

* bulk create nodes I/O

* find schema file

* bulk create edges  I/O

* bulk create edges  I/O

* bulk load io

* no outputs for final tasks

* add recursive glob

* fix globbing

* oops

* delete dags

* pin dug to latest release

* cruft cleanup

* re-org kgx config

* add support for multiple initial repos

* fix comma

* create dir to download to

* swap branch and repo

* clean up dirs

* fix up other pipeline 👌

* add remaining pipelines

* adding ctn parser

* change merge strategy

* merge init fix

* debug dir

* fix topmed file read

* fix topmed file read

* return file names as strings

* topmed kgx builder custom

* topmed kgx builder custom

* add skip

* get files pattern recursive

* version pin avalon

* pin dug

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Co-authored-by: braswent <[email protected]>