Package-ify code

[vchuravy]

Currently the code is mixing dependencies from the package to benchmark with the dependencies for the package itself:

[deps]
ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
Bonito = "824d6782-a2ef-11e9-3a09-e5662e0c26f8"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
WGLMakie = "276b4fcb-3e11-5398-bf8b-a0c2d153d008"

[compat]
ADTypes = "1.18.0"
BenchmarkTools = "1"
Bonito = "3"
JSON = "0.21"
SciMLBase = "1.92.0"
Trixi = "0.8.10"
WGLMakie = "0.9, 0.10"
julia = "1.9

x-ref: https://modernjuliaworkflows.org/writing/#local_packages
x-ref: https://vchuravy.dev/rse-course/mod2_principles_of_rse/github/#Structure-of-a-Julia-Github-repository

Pkg.activate should not be called from within a source file.