diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml
new file mode 100644
index 0000000000..5ffdb3a9bd
--- /dev/null
+++ b/.JuliaFormatter.toml
@@ -0,0 +1,5 @@
+margin = 80
+indent = 4
+always_for_in = true
+whitespace_typedefs = true
+whitespace_ops_in_indices = true
diff --git a/.dev/Manifest-v1.11.toml b/.dev/Manifest-v1.11.toml
deleted file mode 100644
index 220f1226f7..0000000000
--- a/.dev/Manifest-v1.11.toml
+++ /dev/null
@@ -1,121 +0,0 @@
-# This file is machine-generated - editing it directly is not advised
-
-julia_version = "1.11.3"
-manifest_format = "2.0"
-project_hash = "b280bcf3b481823c97fa1a62c1b5e65114b8fa18"
-
-[[deps.Base64]]
-uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
-version = "1.11.0"
-
-[[deps.CSTParser]]
-deps = ["Tokenize"]
-git-tree-sha1 = "0157e592151e39fa570645e2b2debcdfb8a0f112"
-uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f"
-version = "3.4.3"
-
-[[deps.CommonMark]]
-deps = ["Crayons", "PrecompileTools"]
-git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa"
-uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
-version = "0.8.15"
-
-[[deps.Compat]]
-deps = ["TOML", "UUIDs"]
-git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215"
-uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.16.0"
-
-    [deps.Compat.extensions]
-    CompatLinearAlgebraExt = "LinearAlgebra"
-
-    [deps.Compat.weakdeps]
-    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-
-[[deps.Crayons]]
-git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
-uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
-version = "4.1.1"
-
-[[deps.DataStructures]]
-deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82"
-uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.20"
-
-[[deps.Dates]]
-deps = ["Printf"]
-uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
-version = "1.11.0"
-
-[[deps.Glob]]
-git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
-uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
-version = "1.3.1"
-
-[[deps.InteractiveUtils]]
-deps = ["Markdown"]
-uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
-version = "1.11.0"
-
-[[deps.JuliaFormatter]]
-deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "PrecompileTools", "TOML", "Tokenize"]
-git-tree-sha1 = "59cf7ad64f1b0708a4fa4369879d33bad3239b56"
-uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.62"
-
-[[deps.Markdown]]
-deps = ["Base64"]
-uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
-version = "1.11.0"
-
-[[deps.OrderedCollections]]
-git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad"
-uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.7.0"
-
-[[deps.PrecompileTools]]
-deps = ["Preferences"]
-git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
-uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-version = "1.2.1"
-
-[[deps.Preferences]]
-deps = ["TOML"]
-git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
-uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.4.3"
-
-[[deps.Printf]]
-deps = ["Unicode"]
-uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-version = "1.11.0"
-
-[[deps.Random]]
-deps = ["SHA"]
-uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-version = "1.11.0"
-
-[[deps.SHA]]
-uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
-version = "0.7.0"
-
-[[deps.TOML]]
-deps = ["Dates"]
-uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
-version = "1.0.3"
-
-[[deps.Tokenize]]
-git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75"
-uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
-version = "0.5.29"
-
-[[deps.UUIDs]]
-deps = ["Random", "SHA"]
-uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
-version = "1.11.0"
-
-[[deps.Unicode]]
-uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
-version = "1.11.0"
diff --git a/.dev/Manifest.toml b/.dev/Manifest.toml
deleted file mode 100644
index 0d228156f6..0000000000
--- a/.dev/Manifest.toml
+++ /dev/null
@@ -1,113 +0,0 @@
-# This file is machine-generated - editing it directly is not advised
-
-julia_version = "1.10.8"
-manifest_format = "2.0"
-project_hash = "b280bcf3b481823c97fa1a62c1b5e65114b8fa18"
-
-[[deps.Base64]]
-uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
-
-[[deps.CSTParser]]
-deps = ["Tokenize"]
-git-tree-sha1 = "0157e592151e39fa570645e2b2debcdfb8a0f112"
-uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f"
-version = "3.4.3"
-
-[[deps.CommonMark]]
-deps = ["Crayons", "PrecompileTools"]
-git-tree-sha1 = "3faae67b8899797592335832fccf4b3c80bb04fa"
-uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
-version = "0.8.15"
-
-[[deps.Compat]]
-deps = ["TOML", "UUIDs"]
-git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215"
-uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.16.0"
-
-    [deps.Compat.extensions]
-    CompatLinearAlgebraExt = "LinearAlgebra"
-
-    [deps.Compat.weakdeps]
-    Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-    LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-
-[[deps.Crayons]]
-git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15"
-uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
-version = "4.1.1"
-
-[[deps.DataStructures]]
-deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82"
-uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.20"
-
-[[deps.Dates]]
-deps = ["Printf"]
-uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
-
-[[deps.Glob]]
-git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496"
-uuid = "c27321d9-0574-5035-807b-f59d2c89b15c"
-version = "1.3.1"
-
-[[deps.InteractiveUtils]]
-deps = ["Markdown"]
-uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
-
-[[deps.JuliaFormatter]]
-deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "PrecompileTools", "TOML", "Tokenize"]
-git-tree-sha1 = "59cf7ad64f1b0708a4fa4369879d33bad3239b56"
-uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.62"
-
-[[deps.Markdown]]
-deps = ["Base64"]
-uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
-
-[[deps.OrderedCollections]]
-git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad"
-uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.7.0"
-
-[[deps.PrecompileTools]]
-deps = ["Preferences"]
-git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
-uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-version = "1.2.1"
-
-[[deps.Preferences]]
-deps = ["TOML"]
-git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
-uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.4.3"
-
-[[deps.Printf]]
-deps = ["Unicode"]
-uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-
-[[deps.Random]]
-deps = ["SHA"]
-uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-
-[[deps.SHA]]
-uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
-version = "0.7.0"
-
-[[deps.TOML]]
-deps = ["Dates"]
-uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
-version = "1.0.3"
-
-[[deps.Tokenize]]
-git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75"
-uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
-version = "0.5.29"
-
-[[deps.UUIDs]]
-deps = ["Random", "SHA"]
-uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
-
-[[deps.Unicode]]
-uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
diff --git a/.dev/Project.toml b/.dev/Project.toml
deleted file mode 100644
index 71708c8046..0000000000
--- a/.dev/Project.toml
+++ /dev/null
@@ -1,5 +0,0 @@
-[deps]
-JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-
-[compat]
-JuliaFormatter = "1"
diff --git a/.dev/clima_formatter_options.jl b/.dev/clima_formatter_options.jl
deleted file mode 100644
index 1db65e8c7d..0000000000
--- a/.dev/clima_formatter_options.jl
+++ /dev/null
@@ -1,8 +0,0 @@
-clima_formatter_options = (
-    indent = 4,
-    margin = 80,
-    always_for_in = true,
-    whitespace_typedefs = true,
-    whitespace_ops_in_indices = true,
-    remove_extra_newlines = false,
-)
diff --git a/.dev/climaformat.jl b/.dev/climaformat.jl
index 713a5189dd..432b366ef9 100644
--- a/.dev/climaformat.jl
+++ b/.dev/climaformat.jl
@@ -1,85 +1,14 @@
 #!/usr/bin/env julia
-#
-# This is an adapted version of format.jl from JuliaFormatter with the
-# following license:
-#
-#    MIT License
-#    Copyright (c) 2019 Dominique Luna
-#
-#    Permission is hereby granted, free of charge, to any person obtaining a
-#    copy of this software and associated documentation files (the
-#    "Software"), to deal in the Software without restriction, including
-#    without limitation the rights to use, copy, modify, merge, publish,
-#    distribute, sublicense, and/or sell copies of the Software, and to permit
-#    persons to whom the Software is furnished to do so, subject to the
-#    following conditions:
-#
-#    The above copyright notice and this permission notice shall be included
-#    in all copies or substantial portions of the Software.
-#
-#    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-#    OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-#    MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
-#    NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
-#    DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-#    OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
-#    USE OR OTHER DEALINGS IN THE SOFTWARE.
-#
-using Pkg
-Pkg.activate(@__DIR__)
-Pkg.instantiate()
 
-using JuliaFormatter
-
-include("clima_formatter_options.jl")
-
-help = """
-Usage: climaformat.jl [flags] [FILE/PATH]...
-
-Formats the given julia files using the CLIMA formatting options.  If paths
-are given it will format the julia files in the paths. Otherwise, it will
-format all changed julia files.
-
-    -v, --verbose
-        Print the name of the files being formatted with relevant details.
-
-    -h, --help
-        Print this message.
-"""
-
-function parse_opts!(args::Vector{String})
-    i = 1
-    opts = Dict{Symbol, Union{Int, Bool}}()
-    while i ≤ length(args)
-        arg = args[i]
-        if arg[1] != '-'
-            i += 1
-            continue
-        end
-        if arg == "-v" || arg == "--verbose"
-            opt = :verbose
-        elseif arg == "-h" || arg == "--help"
-            opt = :help
-        else
-            error("invalid option $arg")
-        end
-        if opt in (:verbose, :help)
-            opts[opt] = true
-            deleteat!(args, i)
-        end
-    end
-    return opts
-end
-
-opts = parse_opts!(ARGS)
-if haskey(opts, :help)
-    write(stdout, help)
-    exit(0)
-end
-if isempty(ARGS)
-    filenames = readlines(`git ls-files "*.jl"`)
-else
-    filenames = ARGS
-end
-
-format(filenames; clima_formatter_options..., opts...)
+println("climaformat.jl has been discontinued in favor of JuliaFormatter")
+println("To use JuliaFormatter, add it to your base environment with: ")
+println()
+println("julia -e 'using Pkg. Pkg.add(\"JuliaFormatter\")'")
+println()
+println("Then, format your current package with")
+println()
+println("using JuliaFormatter; format(\".\")")
+println()
+println("in a Julia REPL.")
+println("See documentation to read more about this change")
+println("This file will be removed in future releases")
diff --git a/.dev/pre-commit b/.dev/pre-commit
deleted file mode 100644
index 0e56ed0804..0000000000
--- a/.dev/pre-commit
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env julia
-#
-# Called by git-commit with no arguments.  This checks to make sure that all
-# .jl files are indented correctly before a commit is made.
-#
-# To enable this hook, make this file executable and copy it in
-# $GIT_DIR/hooks.
-
-toplevel_directory = chomp(read(`git rev-parse --show-toplevel`, String))
-
-using Pkg
-Pkg.activate(joinpath(toplevel_directory, ".dev"))
-Pkg.instantiate()
-
-using JuliaFormatter
-
-include(joinpath(toplevel_directory, ".dev", "clima_formatter_options.jl"))
-
-needs_format = false
-
-for diffoutput in split.(readlines(`git diff --name-status --cached`))
-    status = diffoutput[1]
-    filename = diffoutput[end]
-    (!startswith(status, "D") && endswith(filename, ".jl")) || continue
-
-    a = read(`git show :$filename`, String)
-    b = format_text(a; clima_formatter_options...)
-
-    if a != b
-        fullfilename = joinpath(toplevel_directory, filename)
-
-        @error """File $filename needs to be indented with:
-            julia $(joinpath(toplevel_directory, ".dev", "climaformat.jl")) $fullfilename
-        and added to the git index via
-            git add $fullfilename
-        """
-        global needs_format = true
-    end
-end
-
-exit(needs_format ? 1 : 0)
diff --git a/.dev/up_deps.jl b/.dev/up_deps.jl
index 2ca708eb2c..295c6b1a5c 100644
--- a/.dev/up_deps.jl
+++ b/.dev/up_deps.jl
@@ -1,36 +1,12 @@
-#=
-A simple script for updating the manifest
-files in all of our environments.
-=#
+#!/usr/bin/env julia
 
-root = dirname(@__DIR__)
-dirs = (
-    root,
-    joinpath(root, "test"),
-    joinpath(root, ".dev"),
-    joinpath(root, "perf"),
-    joinpath(root, "docs"),
-    joinpath(root, "examples"),
-)
-
-cd(root) do
-    for dir in dirs
-        reldir = relpath(dir, root)
-        @info "Updating environment `$reldir`"
-        cmd = if dir == root
-            `$(Base.julia_cmd()) --project -e """import Pkg; Pkg.update()"""`
-        elseif dir == joinpath(root, ".dev")
-            `$(Base.julia_cmd()) --project=$reldir -e """import Pkg; Pkg.update()"""`
-        else
-            `$(Base.julia_cmd()) --project=$reldir -e """import Pkg; Pkg.develop(;path=\".\"); Pkg.update()"""`
-        end
-        run(cmd)
-    end
-end
-
-# https://github.com/JuliaLang/Pkg.jl/issues/3014
-for dir in dirs
-    cd(dir) do
-        rm("LocalPreferences.toml"; force = true)
-    end
-end
+println("up_dev.jl has been discontinued in favor of PkgDevTools")
+println("To use PkgDevTool, add it to your base environment with: ")
+println()
+println("julia -e 'using Pkg. Pkg.add(\"PkgDevTools\")'")
+println()
+println("Then, update the manifests with")
+println("using PkgDevTools; PkgDevToos.update_deps(\".\")")
+println("in a Julia REPL.")
+println("See documentation to read more about this change")
+println("This file will be removed in future releases")
diff --git a/.github/workflows/julia_formatter.yml b/.github/workflows/julia_formatter.yml
index 2c9262176b..aa58b9dd05 100644
--- a/.github/workflows/julia_formatter.yml
+++ b/.github/workflows/julia_formatter.yml
@@ -1,41 +1,14 @@
 name: JuliaFormatter
 
 on:
-  push:
-    tags: '*'
   pull_request:
-  merge_group:
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: true
-
+    # this argument is not required if you don't use the `suggestion-label` input
+    types: [ opened, reopened, synchronize, labeled, unlabeled ]
 jobs:
   format:
     runs-on: ubuntu-latest
-    timeout-minutes: 30
     steps:
-
-    - uses: actions/checkout@v4
-
-    - uses: dorny/paths-filter@v3.0.2
-      id: filter
-      with:
-        filters: |
-          julia_file_change:
-            - added|modified: '**.jl'
-
-    - uses: julia-actions/setup-julia@v2
-      if: steps.filter.outputs.julia_file_change == 'true'
-      with:
-        version: '1.10'
-
-    - name: Apply JuliaFormatter
-      if: steps.filter.outputs.julia_file_change == 'true'
-      run: |
-        julia --project=.dev .dev/climaformat.jl .
-
-    - name: Check formatting diff
-      if: steps.filter.outputs.julia_file_change == 'true'
-      run: |
-        git diff --color=always --exit-code
+      - uses: julia-actions/julia-format@v3
+        with:
+          version: '1' # Set `version` to '1.0.54' if you need to use JuliaFormatter.jl v1.0.54 (default: '1')
+          suggestion-label: 'format-suggest' # leave this unset or empty to show suggestions for all PRs
diff --git a/NEWS.md b/NEWS.md
index cb2f6a466a..d44232c0f9 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,14 @@ ClimaAtmos.jl Release Notes
 Main
 -------
 
+### Development
+
+The `.dev` was deprecated. The two utilities in this folder can be replaced with
+more established and better developed tools:
+- instead of `clima_format`, use `JuliaFormatter`,
+- instead of `up_deps`, use `PkgDevTools`.
+See the  [documentation](https://clima.github.io/ClimaAtmos.jl/dev/contributor_guide/#Formatting) for more information.
+
 ### Features
 
 ### Read CO2 from file
diff --git a/docs/src/contributor_guide.md b/docs/src/contributor_guide.md
index 14a576bc1b..b3160bd0ae 100644
--- a/docs/src/contributor_guide.md
+++ b/docs/src/contributor_guide.md
@@ -180,6 +180,59 @@ and then open `docs/build/index.html` in your favorite browser. Providing the en
 `JULIA_DEBUG=Documenter` will provide with more information in the documentation build process and
 thus help figuring out a potential bug.
 
+## Formatting
+
+One of the tests consists in checking that the code is uniformly formatted. We
+use [JuliaFormatter.jl](https://github.com/domluna/JuliaFormatter.jl) to achieve
+consistent formatting. Here's how to use it:
+
+You can install in your base environment with
+``` sh
+julia -e 'using Pkg; Pkg.add("JuliaFormatter")'
+```
+alongside your other development tools.
+
+Then, you can format the package running:
+``` julia
+using JuliaFormatter; format(".")
+```
+or just with `format(".")` if the package is already imported.
+
+The rules for formatting are defined in the `.JuliaFormatter.toml`.
+
+If you are used to formatting from the command line instead of the REPL, you can
+install `JuliaFormatter` in your base environment and call
+``` sh
+julia -e 'using JuliaFormatter; format(".")'
+```
+You could also define a shell alias
+``` sh
+alias julia_format_here="julia -e 'using JuliaFormatter; format(\".\")'"
+```
+
+!!! note
+
+In the past, `ClimaAtmos` used to have a `.dev/climaformat.jl` script. We moved
+away from it to reduce complexity in our repository and to align with the
+general tools used by the Julia community. If you are still using
+`climaformat.jl`, migrate to `JuliaFormatter` (`climaformat.jl` was just a
+wrapper around `JuliaFormatter`).
+
+## Updating environments
+
+The repository for `ClimaAtmos` includes several checked `Manifests.toml`. This
+is to help with reproducing results.
+[PkgDevTools](https://github.com/CliMA/PkgDevTools.jl) provides a convenient
+system to quickly update all the `Manifests.toml`. Please, refer to the
+documentation for more information.
+
+!!! note
+
+In the past, `ClimaAtmos` used to have a `.dev/up_deps.jl` script. We moved away
+from it because `PkgDevTools` provides a much simpler and more efficient way to
+accomplish the same result.
+
+
 ## Credits
 
 This contributor's guide is heavily based on the excellent [Oceananigans.jl contributor's guide](https://clima.github.io/OceananigansDocumentation/stable/contributing/) which is heavily based on the excellent [MetPy contributor's guide](https://github.com/Unidata/MetPy/blob/master/CONTRIBUTING.md).