Update to Lean v4.6.0

[eyihluyc]

This pull request updates occurrences of decreasing_by to align with its updated semantics since Lean v4.6.0-rc1. Previously, the tactic that followed decreasing_by (in our case, sorry) was applied to all goals. With the update, it's possible to use different tactics for individual goals.

Also this PR contains a fix to the order of the dependencies in lakefile.lean, thanks to the people from the Lean community. Otherwise, there was an error in the generation of the documentation. More details on this can be found in the discussion on Zulip.

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PR-Codex overview

The focus of this PR is to update dependencies and refine code in the phi-calculus package.

Detailed summary

• Updated leanprover/lean4 to v4.6.0-rc1
• Removed unnecessary mathlib and std dependencies
• Refactored Calculus.lean with decreasing_by all_goals sorry
• Updated dependencies in lake-manifest.json

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