Fix CLI to work with DataChain new listing

[ilongin]

This PR fixes all CLI methods to work with new listing of DataChain by using .from_storage() method.
Before, CLI was completely detached which means if you would do datachain index, listing created by that command would be invisible by DataChain lib, and vice versa.
Now, those are again "one" system.

Followups:

• Clean obsolete storage, partials and maybe id generation tables #536
• Fix tests that are skipped #535

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[codecov]

Codecov Report

Attention: Patch coverage is 91.79104% with 11 lines in your changes missing coverage. Please review.

Project coverage is 86.92%. Comparing base (34e7c2b) to head (1cd59b8).

Files with missing lines	Patch %	Lines
src/datachain/data_storage/warehouse.py	85.71%	6 Missing ⚠️
src/datachain/lib/dc.py	88.00%	3 Missing ⚠️
src/datachain/data_storage/sqlite.py	33.33%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #517      +/-   ##
==========================================
- Coverage   87.39%   86.92%   -0.48%     
==========================================
  Files          97       97              
  Lines       10197    10135      -62     
  Branches     1396     1384      -12     
==========================================
- Hits         8912     8810     -102     
- Misses        923      961      +38     
- Partials      362      364       +2     

Flag	Coverage Δ
datachain	86.86% <91.79%> (-0.48%)	⬇️

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