feat: add index persistence

[stephantul]

This PR adds index persistence for use in the CLI, which is a feature requested by several users.

This is a big PR! Sorry for that. This PR:

• Adds a new index command to the CLI.

You can now index a repository as follows:

semble index -o "my_index"

and then search using:

semble search "where is persistency defined?" --index "my_index"

This greatly speeds up subsequent searches. Loading a decently-sized index takes 200-400ms.

• Adds persistence to the embedding backend. This was necessary because we override the basicbackend a little weirdly. Something we can think about doing differently
• Adds persistence to the index itself. All components are saved in subfolders, except the model. For the model, we save the name of the model. To facilitate saving itself, I added helpers to Chunk. These are thin wrappers around asdict and a dictionary expansion.
• Removed the Encoder protocol: this no longer made sense because we use the saving and loading methods in model2vec.

The ugly part of this is that I chose to refactor a large part of the code: we now now longer pass a model to the index when building it. Instead I use a path to the model. This path is then used to load the model, and reverts to the default model when None. This is a more elegant construction I think, since this allows us to store the model path, and also cache model loading more efficiently.

Follow-up tasks:

• Not all benchmarks work, but the most important ones (i.e., the regular one and ablations) still work.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
src/semble/__init__.py	100.00% <100.00%> (ø)
src/semble/cli.py	100.00% <100.00%> (ø)
src/semble/index/create.py	100.00% <100.00%> (ø)
src/semble/index/dense.py	100.00% <100.00%> (ø)
src/semble/index/index.py	100.00% <100.00%> (ø)
src/semble/index/types.py	100.00% <100.00%> (ø)
src/semble/mcp.py	100.00% <100.00%> (ø)
src/semble/search.py	100.00% <100.00%> (ø)
src/semble/types.py	100.00% <100.00%> (ø)
src/semble/utils.py	100.00% <100.00%> (ø)

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[Pringled]

Very very nice, some minor things