Add a separate option to run the API server using mmap

[tibvdm]

Important

This PR can only be merged, when all other PR's in other repositories are merged:
unipept/unipept-index#34
unipept/unipept-utilities#2

Before merging, the dependencies need to be updated to point to the main branch. Right now they point to a separate branch for testing purposes

This pull request updates how the index and protein data are loaded in the API, introducing support for memory-mapped file loading and switching to new binary file formats for improved speed and efficiency. The most important changes are grouped below:

Index and Data Loading Improvements:

• The start function in api/src/lib.rs now takes a use_mmap boolean parameter, allowing the API to load index files using memory-mapped I/O for faster access. This parameter is also exposed as a command-line argument (--mmap) in api/src/main.rs.
• The index now loads protein and mapping data from new binary files (proteins.bin and mapping.bin instead of proteins.tsv), and uses updated loader functions from the new sa_server dependency.
• The construction of the Index object is updated to use the new Searcher structure, taking advantage of the new mapping file and memory-mapped loading.

Code Cleanup:

• Old code for loading the suffix array from text and compressed formats is removed, as this is now handled by the new loader functions.

[Copilot]

Pull request overview

This PR updates the API/index loading pipeline to support optional memory-mapped file I/O and to load the index’s protein/mapping data from new binary formats, aiming to improve startup and query performance.

Changes:

• Add a --mmap CLI option and plumb it through api::start into index loading.
• Switch index construction to use sa_server loader functions and new binary inputs (proteins.bin, mapping.bin).
• Update dependencies/lockfile to new unipept-index crates and introduce sa-server.

Reviewed changes

Copilot reviewed 4 out of 5 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
index/src/lib.rs	Switches index loading to sa_server loaders and constructs the new Searcher with a mapping file + use_mmap.
index/Cargo.toml	Replaces prior deps with sa-server (and pins several deps to a feature branch).
api/src/main.rs	Adds --mmap flag and passes it into start(...).
api/src/lib.rs	Updates start(...) signature and switches expected index data files to .bin + mapping input.
Cargo.lock	Updates git dependency sources and adds memmap2/sa-server transitive deps.

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[SimonVandeVyver]

I looked at the code and ran the api, everything worked as expected.
I performed some API calls while using the mmap feature, with the mmap feature disables and using the develop branch, which all return the same results

[SimonVandeVyver]

The branch of the dependency is still using the feature branch