diff --git a/reproducibility_tests/reproducibility_tools.jl b/reproducibility_tests/reproducibility_tools.jl
index 0ecb8844b5..bb11a881e1 100644
--- a/reproducibility_tests/reproducibility_tools.jl
+++ b/reproducibility_tests/reproducibility_tools.jl
@@ -180,7 +180,8 @@ function reproducibility_results(
         :no_comparable_dirs,
     )
 
-    data_file_references = map(p -> joinpath(p, reference_filename), dirs)
+    data_file_references =
+        map(p -> joinpath(p, job_id, reference_filename), dirs)
 
     # foreach(x->maybe_extract(x), data_file_references)
 
@@ -203,6 +204,11 @@ function reproducibility_results(
                 dict_reference = dict_reference_solution,
             )
         end
+    if debug_reproducibility()
+        println("------ end of reproducibility_results")
+        @show computed_mses
+        println("------")
+    end
     return (dirs, computed_mses, :successful_comparison)
 end
 
@@ -275,8 +281,9 @@ function export_reproducibility_results(
         skip,
     )
 
+    commit_shas = readdir(save_dir)
     for (computed_mse, dir) in zip(computed_mses, dirs)
-        commit_hash = basename(dirname(dir))
+        commit_hash = commit_sha_from_dir(commit_shas, dir)
         computed_mse_file =
             joinpath(repro_dir, "computed_mse_$commit_hash.json")
 
@@ -287,6 +294,15 @@ function export_reproducibility_results(
     return (data_file_computed, computed_mses, dirs, how)
 end
 
+function commit_sha_from_json_file(file)
+    filename = basename(file)
+    if startswith(filename, "computed_mse_") && endswith(filename, ".json")
+        return replace(filename, "computed_mse_" => "", ".json" => "")
+    else
+        error("File $file does not follow correct format.")
+    end
+end
+
 import ClimaReproducibilityTests as CRT
 using Test
 import PrettyTables
@@ -367,6 +383,11 @@ function report_reproducibility_results(
 
     for computed_mse in computed_mses
         all_reproducible = true
+        if debug_reproducibility()
+            println("---- in report_reproducibility_results")
+            @show computed_mse
+            println("----")
+        end
         for (var, reproducible) in CRT.test_mse(; computed_mse)
             if !reproducible
                 all_reproducible = false
@@ -420,8 +441,9 @@ function report_reproducibility_results(
     table_data = hcat(sources, summary_statuses)
     PrettyTables.pretty_table(io, table_data; header, crop = :none)
 
+    n_comparisons = length(computed_mses)
     println(io, "Summary:")
-    println(io, "   n_comparisons                = $(length(computed_mses))")
+    println(io, "   n_comparisons                = $n_comparisons")
     println(io, "   n_times_reproducible         = $n_times_reproducible")
     println(io, "   n_times_not_reproducible     = $n_times_not_reproducible")
     println(io, "   n_passes                     = $n_passes")
@@ -440,7 +462,7 @@ function report_reproducibility_results(
     elseif test_broken_report_flakiness
         return :not_yet_reproducible
     else
-        if n_passes ≥ n_pass_limit
+        if n_passes ≥ n_pass_limit || n_passes == n_comparisons
             return :reproducible
         else
             return :not_reproducible
diff --git a/reproducibility_tests/reproducibility_utils.jl b/reproducibility_tests/reproducibility_utils.jl
index 3e08beb0bc..306e38bae4 100644
--- a/reproducibility_tests/reproducibility_utils.jl
+++ b/reproducibility_tests/reproducibility_utils.jl
@@ -51,10 +51,9 @@ assist our understanding and reasoning, we let's assume that there are two state
 
 ## state 2: data is saved for future reference
 
- - `commit_hash/job_id/output_dir/`
- - `commit_hash/job_id/output_dir/reproducibility_bundle/`
- - `commit_hash/job_id/output_dir/reproducibility_bundle/ref_counter.jl`
- - `commit_hash/job_id/output_dir/reproducibility_bundle/prog_state.hdf5`
+ - `commit_hash/job_id/reproducibility_bundle/`
+ - `commit_hash/job_id/reproducibility_bundle/ref_counter.jl`
+ - `commit_hash/job_id/reproducibility_bundle/prog_state.hdf5`
 
  - `commit_hash/reproducibility_bundle/ref_counter.jl`
  - `commit_hash/reproducibility_bundle/job_id/`
@@ -458,12 +457,12 @@ print_dir_tree(dir) = print_dir_tree(stdout, dir)
 print_dir_tree(io::IO, dir) = println(io, string_dir_tree(dir))
 
 function string_dir_tree(dir)
-    s = "Files in `$dir`\n:"
+    s = "Files in `$dir`:\n"
     for (root, _, files) in walkdir(dir)
         for file in files
             f = joinpath(root, file)
             isfile(f) || continue # rm symlink folders (included but not files)
-            s *= "  $f\n"
+            s *= "  $(replace(f, dir => ""))\n"
         end
     end
     return s
@@ -480,8 +479,7 @@ end
         ref_counter_PR = read_ref_counter(ref_counter_file_PR),
         skip = get(ENV, "BUILDKITE_PIPELINE_SLUG", nothing) != "climaatmos-ci",
         dest_root = "/central/scratch/esm/slurm-buildkite/climaatmos-main",
-        commit = get(ENV, "BUILDKITE_COMMIT", nothing),
-        n_hash_characters = 7,
+        commit = get_commit_sha(),
         repro_folder = "reproducibility_bundle",
         strip_folder = strip_output_active_path,
     )
@@ -519,8 +517,7 @@ function move_data_to_save_dir(;
     ref_counter_PR = read_ref_counter(ref_counter_file_PR),
     skip = get(ENV, "BUILDKITE_PIPELINE_SLUG", nothing) != "climaatmos-ci",
     dest_root = "/central/scratch/esm/slurm-buildkite/climaatmos-main",
-    commit = get(ENV, "BUILDKITE_COMMIT", nothing),
-    n_hash_characters = 7,
+    commit = get_commit_sha(),
     repro_folder = "reproducibility_bundle",
     strip_folder = strip_output_active_path,
 )
@@ -541,36 +538,20 @@ function move_data_to_save_dir(;
             dirs_src,
             dest_root,
             commit,
-            n_hash_characters,
             repro_folder,
             strip_folder,
         )
         if debug_reproducibility()
-            @show repro_folder
-            @show dirs_src
-            @show dest_root
-            @show files_dest
-            @show files_src
-            @show isfile.(files_src)
             println("******")
             foreach(print_dir_tree, dirs_src)
             println("******")
-            print_dir_tree(dest_root)
-            println("******")
         end
         for (src, dest) in zip(files_src, files_dest)
-            @show src
-            @show dest
             @assert isfile(src)
             mkpath(dirname(dest))
             mv(src, dest; force = true)
         end
-        dest_repro = destination_directory(;
-            dest_root,
-            commit,
-            n_hash_characters,
-            repro_folder,
-        )
+        dest_repro = destination_directory(; dest_root, commit, repro_folder)
         ref_counter_file_main = joinpath(dest_repro, "ref_counter.jl")
         debug_reproducibility() &&
             @info "Repro: moving $ref_counter_file_PR to $ref_counter_file_main"
@@ -590,14 +571,40 @@ function move_data_to_save_dir(;
     end
 end
 
+"""
+    get_commit_sha(;
+        n_hash_characters = 7,
+        commit = get(ENV, "BUILDKITE_COMMIT", nothing)
+    )
+
+Returns a string of the commit hash.
+"""
+get_commit_sha(;
+    n_hash_characters = 7,
+    commit = get(ENV, "BUILDKITE_COMMIT", nothing),
+) = return commit[1:min(n_hash_characters, length(commit))]
+
+function commit_sha_from_dir(commit_shas, dir)
+    while true
+        if isempty(dir)
+            error("Unfound commit sha.")
+        else
+            b = basename(dir)
+            if b in commit_shas || any(x -> occursin(b, x), commit_shas)
+                return b
+            else
+                dir = dirname(dir)
+            end
+        end
+    end
+end
 
 """
     save_dir_transform(
         src;
         job_id,
         dest_root = "/central/scratch/esm/slurm-buildkite/climaatmos-main",
-        commit = get(ENV, "BUILDKITE_COMMIT", nothing),
-        n_hash_characters = 7,
+        commit = get_commit_sha(),
         repro_folder = "reproducibility_bundle",
         strip_folder = strip_output_active_path,
     )
@@ -607,7 +614,6 @@ Returns the output file, to be saved, given:
  - `job_id` the job ID
  - `dest_root` the destination root directory
  - `commit` the commit hash
- - `n_hash_characters` truncates the commit hash to given number of characters
  - `repro_folder` reproducibility folder
  - `strip_folder` function to strip folders in output path
 """
@@ -615,17 +621,11 @@ function save_dir_transform(
     src;
     job_id,
     dest_root = "/central/scratch/esm/slurm-buildkite/climaatmos-main",
-    commit = get(ENV, "BUILDKITE_COMMIT", nothing),
-    n_hash_characters = 7,
+    commit = get_commit_sha(),
     repro_folder = "reproducibility_bundle",
     strip_folder = strip_output_active_path,
 )
-    dest_repro = destination_directory(;
-        dest_root,
-        commit,
-        n_hash_characters,
-        repro_folder,
-    )
+    dest_repro = destination_directory(; dest_root, commit, repro_folder)
     src_filename = basename(src)
     dst = joinpath(dest_repro, job_id, src_filename)
     return strip_output_active_path(dst)
@@ -634,8 +634,7 @@ end
 """
     destination_directory(;
         dest_root = "/central/scratch/esm/slurm-buildkite/climaatmos-main",
-        commit = get(ENV, "BUILDKITE_COMMIT", nothing),
-        n_hash_characters = 7,
+        commit = get_commit_sha(),
         repro_folder = "reproducibility_bundle",
     )
 
@@ -643,17 +642,14 @@ Return the reproducibility destination directory:
 `root/commit_sha/repro_folder`, given:
  - `dest_root` the destination root directory
  - `commit` the commit hash
- - `n_hash_characters` truncates the commit hash to given number of characters
  - `repro_folder` reproducibility folder
 """
 function destination_directory(;
     dest_root = "/central/scratch/esm/slurm-buildkite/climaatmos-main",
-    commit = get(ENV, "BUILDKITE_COMMIT", nothing),
-    n_hash_characters = 7,
+    commit = get_commit_sha(),
     repro_folder = "reproducibility_bundle",
 )
-    commit_sha = commit[1:min(n_hash_characters, length(commit))]
-    return joinpath(dest_root, commit_sha, repro_folder)
+    return joinpath(dest_root, commit, repro_folder)
 end
 
 """
diff --git a/reproducibility_tests/test_mse.jl b/reproducibility_tests/test_mse.jl
index 7e586b2059..f1b35cceea 100644
--- a/reproducibility_tests/test_mse.jl
+++ b/reproducibility_tests/test_mse.jl
@@ -12,11 +12,10 @@ include(joinpath(@__DIR__, "reproducibility_tools.jl"))
 
 debug = true
 repro_dir = joinpath(out_dir, "reproducibility_bundle")
-computed_mse_filenames =
-    map(filter(default_is_mse_file, readdir(repro_dir))) do x
-        joinpath(repro_dir, x)
-    end
-if isempty(computed_mse_filenames)
+computed_mse_files = map(filter(default_is_mse_file, readdir(repro_dir))) do x
+    joinpath(repro_dir, x)
+end
+if isempty(computed_mse_files)
     @warn "No reproducibility tests performed, due to non-existent comparable data."
     debug && @show readdir(out_dir)
     debug && @show readdir(repro_dir)
@@ -61,10 +60,16 @@ if isempty(computed_mse_filenames)
 else
     @testset "Reproducibility tests" begin
         commit_hashes =
-            map(x -> basename(dirname(dirname(x))), computed_mse_filenames)
+            map(x -> commit_sha_from_json_file(x), computed_mse_files)
+        computed_mses = map(x -> parse_file_json(x), computed_mse_files)
+        if debug_reproducibility()
+            println("------ in test_mse.jl")
+            @show computed_mses
+            println("------")
+        end
         results = report_reproducibility_results(
             commit_hashes,
-            computed_mse_filenames;
+            computed_mses;
             test_broken_report_flakiness,
         )
 
diff --git a/test/unit_reproducibility_infra.jl b/test/unit_reproducibility_infra.jl
index 5afe803d3d..ae58f5826d 100644
--- a/test/unit_reproducibility_infra.jl
+++ b/test/unit_reproducibility_infra.jl
@@ -687,7 +687,6 @@ end
     make_and_cd() do dir
         job_id = "job_id"
         commit = "commit_sha"
-        n_hash_characters = 10
         output = "output_active"
         strip_folder = output
         repro_folder = "rbundle"
@@ -698,14 +697,12 @@ end
             dest_root = dir,
             job_id,
             commit,
-            n_hash_characters,
             repro_folder,
             strip_folder,
         ) == joinpath(dir, dst)
 
         job_id = "job_id"
         commit = "commit_sha"
-        n_hash_characters = 10
         output = "output_active"
         strip_folder = output
         repro_folder = "rbundle"
@@ -716,7 +713,6 @@ end
             dest_root = dir,
             job_id,
             commit,
-            n_hash_characters,
             repro_folder,
             strip_folder,
         ) == joinpath(dir, dst)
@@ -734,6 +730,15 @@ end
           joinpath("a", "output_1A34", "c")
 end
 
+@testset "Reproducibility infrastructure: commit_sha_from_json_file" begin
+    @test_throws ErrorException commit_sha_from_json_file(
+        joinpath("a", "b", "c"),
+    )
+    @test commit_sha_from_json_file(
+        joinpath("a", "b", "computed_mse_H123.json"),
+    ) == "H123"
+end
+
 @testset "Reproducibility infrastructure: save_dir_in_out_list" begin
     mktempdir2_cd_computed() do (save_dir, computed_dir)
         hash1 = joinpath(save_dir, "hash1")
@@ -772,7 +777,6 @@ end
             dirs_src = [job_id_1, job_id_2],
             dest_root = save_dir,
             commit = "commit_sha",
-            n_hash_characters = 10,
             repro_folder,
             strip_folder = "output_active",
         )
@@ -847,7 +851,6 @@ end
             dest_root = save_dir,
             buildkite_ci = true,
             commit = "hash_new",
-            n_hash_characters = length("hash_new"),
             branch = "unit_test_move_data_to_save_dir",
             in_merge_queue = true,
             dirs_src = [job_id_1, job_id_2],
@@ -905,7 +908,6 @@ end
             dest_root = save_dir,
             buildkite_ci = true,
             commit = "hash_new",
-            n_hash_characters = length("hash_new"),
             branch = "unit_test_move_data_to_save_dir",
             in_merge_queue = true,
             dirs_src = [job_id_1, job_id_2],
@@ -964,7 +966,6 @@ end
             dest_root = save_dir,
             buildkite_ci = true,
             commit = "hash_new",
-            n_hash_characters = length("hash_new"),
             branch = "unit_test_move_data_to_save_dir",
             in_merge_queue = true,
             dirs_src = [job_id_1, job_id_2],
@@ -982,6 +983,41 @@ end
         @test isfile(joinpath(repro_dir, "ref_counter.jl"))
     end
 end
+@testset "Reproducibility infrastructure: commit_sha_from_dir" begin
+    @test commit_sha_from_dir(
+        ["CH1", "CH2", "CH3"],
+        joinpath("a", "b", "c", "CH1", "e", "f"),
+    ) == "CH1"
+    @test commit_sha_from_dir(
+        ["CH1", "CH2", "CH3"],
+        joinpath("a", "b", "c", "CH2", "e", "f"),
+    ) == "CH2"
+    @test commit_sha_from_dir(
+        ["CH1", "CH2", "CH3"],
+        joinpath("a", "b", "c", "e", "f", "CH2"),
+    ) == "CH2"
+    @test commit_sha_from_dir(
+        ["CH1", "CH2", "CH3"],
+        joinpath("CH2", "a", "b", "c", "e", "f"),
+    ) == "CH2"
+
+    @test commit_sha_from_dir(
+        ["CH1_xyz", "CH2_xyz", "CH3_xyz"],
+        joinpath("a", "b", "c", "CH1", "e", "f"),
+    ) == "CH1"
+    @test commit_sha_from_dir(
+        ["CH1_xyz", "CH2_xyz", "CH3_xyz"],
+        joinpath("a", "b", "c", "CH2", "e", "f"),
+    ) == "CH2"
+    @test commit_sha_from_dir(
+        ["CH1_xyz", "CH2_xyz", "CH3_xyz"],
+        joinpath("a", "b", "c", "e", "f", "CH2"),
+    ) == "CH2"
+    @test commit_sha_from_dir(
+        ["CH1_xyz", "CH2_xyz", "CH3_xyz"],
+        joinpath("CH2", "a", "b", "c", "e", "f"),
+    ) == "CH2"
+end
 
 using ClimaComms
 using ClimaCore: Spaces, Fields, Grids, InputOutput
@@ -1019,8 +1055,18 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
         end
     end
 
+    # ## state 1: end of simulation, folder structure
+    #  - `job_id/output_dir/`
+    #  - `job_id/output_dir/reproducibility_bundle/`
+    #  - `job_id/output_dir/reproducibility_bundle/ref_counter.jl`
+    #  - `job_id/output_dir/reproducibility_bundle/prog_state.hdf5`
+    # ## state 2: data is saved for future reference
+    #  - `commit_hash/job_id/reproducibility_bundle/`
+    #  - `commit_hash/job_id/reproducibility_bundle/ref_counter.jl`
+    #  - `commit_hash/job_id/reproducibility_bundle/prog_state.hdf5`
+
     @testset "Reproducibility infrastructure: reproducibility_results - legacy folder structure" begin
-        make_and_cd() do dir
+        mktempdir2_cd_computed() do (save_dir, computed_dir)
             grid = ExtrudedCubedSphereGrid(;
                 z_elem = 5,
                 z_min = 0,
@@ -1033,19 +1079,25 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
                 Spaces.ExtrudedFiniteDifferenceSpace(grid, Grids.CellCenter())
             comms_ctx = ClimaComms.context(space)
 
+            # Folder structure:
+            job_id = "unit_test"
+            rfolder = "rbundle"
+            output = "output_active"
+            repro_dir = joinpath(computed_dir, job_id, output, rfolder)
+            mkpath(repro_dir)
+
             fv = Fields.FieldVector(; x = ones(space), y = ones(space))
-            file = joinpath(dir, "my_prog_state.hdf5")
+            file = joinpath(repro_dir, "my_prog_state.hdf5")
             hdfwriter = InputOutput.HDF5Writer(file, comms_ctx)
             InputOutput.write!(hdfwriter, fv, "Y")
             Base.close(hdfwriter)
 
             # Not on buildkite
-            job_id = "unit_test"
             (d, v, how) = reproducibility_results(
                 comms_ctx;
                 job_id,
                 name = "Y",
-                save_dir = dir,
+                save_dir = save_dir,
                 ref_counter_PR = 1,
                 reference_filename = "my_prog_state.hdf5",
                 data_file_computed = file,
@@ -1066,7 +1118,7 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
                 comms_ctx;
                 job_id,
                 name = "Y",
-                save_dir = dir,
+                save_dir = save_dir,
                 reference_filename = "my_prog_state.hdf5",
                 ref_counter_PR = 1,
                 data_file_computed = file,
@@ -1083,26 +1135,111 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
 
             # Successful comparison
 
-            d01 = make_ref_file_counter(1, dir, "01")
-            d02 = make_ref_file_counter(2, dir, "02")
-            d03 = make_ref_file_counter(3, dir, "03")
-            d04 = make_ref_file_counter(3, dir, "04")
-            d05 = make_ref_file_counter(3, dir, "05")
-
-            put_data_file(d01, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d02, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d03, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d04, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            commit_sha_01 = "commit_hash_01"
+            commit_sha_02 = "commit_hash_02"
+            commit_sha_03 = "commit_hash_03"
+            commit_sha_04 = "commit_hash_04"
+            commit_sha_05 = "commit_hash_05"
+            d01 = make_ref_file_counter(1, save_dir, commit_sha_01, rfolder)
+            d02 = make_ref_file_counter(2, save_dir, commit_sha_02, rfolder)
+            d03 = make_ref_file_counter(3, save_dir, commit_sha_03, rfolder)
+            d04 = make_ref_file_counter(3, save_dir, commit_sha_04, rfolder)
+            d05 = make_ref_file_counter(3, save_dir, commit_sha_05, rfolder)
+
+            put_data_file(
+                joinpath(d01, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d02, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d03, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d04, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
             fv.x .= 200
             fv.y .= 300
-            put_data_file(d05, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            put_data_file(
+                joinpath(d05, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+
+            # Test folder structure
+            @test isfile(
+                joinpath(
+                    computed_dir,
+                    job_id,
+                    output,
+                    rfolder,
+                    "my_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_01,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_02,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_03,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_04,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_05,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
 
-            job_id = "unit_test"
             (d, v, how) = reproducibility_results(
                 comms_ctx;
                 job_id,
                 name = "Y",
-                save_dir = dir,
+                save_dir = save_dir,
                 ref_counter_PR = 3,
                 reference_filename = "ref_prog_state.hdf5",
                 data_file_computed = file,
@@ -1138,18 +1275,21 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
             comms_ctx = ClimaComms.context(space)
 
             fv = Fields.FieldVector(; x = ones(space), y = ones(space))
-            file = joinpath(
-                computed_dir,
-                "reproducibility_bundle",
-                "computed_prog_state.hdf5",
-            )
-            mkpath(dirname(file))
+
+            # Folder structure:
+            job_id = "unit_test"
+            rfolder = "rbundle"
+            output = "output_active"
+            repro_dir = joinpath(computed_dir, job_id, output, rfolder)
+            mkpath(repro_dir)
+
+            file = joinpath(repro_dir, "computed_prog_state.hdf5")
+            mkpath(repro_dir)
             hdfwriter = InputOutput.HDF5Writer(file, comms_ctx)
             InputOutput.write!(hdfwriter, fv, "Y")
             Base.close(hdfwriter)
 
             # Not on buildkite
-            job_id = "unit_test"
             (d, v, how) = reproducibility_results(
                 comms_ctx;
                 job_id,
@@ -1170,7 +1310,6 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
             @test how == :skipped
 
             # Empty comparable dirs
-            job_id = "unit_test"
             (d, v, how) = reproducibility_results(
                 comms_ctx;
                 job_id,
@@ -1192,19 +1331,49 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
 
             # Successful comparison
 
-            d01 = make_ref_file_counter(1, save_dir, rbundle("01"))
-            d02 = make_ref_file_counter(2, save_dir, rbundle("02"))
-            d03 = make_ref_file_counter(3, save_dir, rbundle("03"))
-            d04 = make_ref_file_counter(3, save_dir, rbundle("04"))
-            d05 = make_ref_file_counter(3, save_dir, rbundle("05"))
-
-            put_data_file(d01, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d02, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d03, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d04, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            commit_sha_01 = "commit_hash_01"
+            commit_sha_02 = "commit_hash_02"
+            commit_sha_03 = "commit_hash_03"
+            commit_sha_04 = "commit_hash_04"
+            commit_sha_05 = "commit_hash_05"
+            d01 = make_ref_file_counter(1, save_dir, commit_sha_01, rfolder)
+            d02 = make_ref_file_counter(2, save_dir, commit_sha_02, rfolder)
+            d03 = make_ref_file_counter(3, save_dir, commit_sha_03, rfolder)
+            d04 = make_ref_file_counter(3, save_dir, commit_sha_04, rfolder)
+            d05 = make_ref_file_counter(3, save_dir, commit_sha_05, rfolder)
+
+            put_data_file(
+                joinpath(d01, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d02, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d03, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d04, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
             fv.x .= 200
             fv.y .= 300
-            put_data_file(d05, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            put_data_file(
+                joinpath(d05, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
 
             job_id = "unit_test"
             (d, v, how) = reproducibility_results(
@@ -1229,6 +1398,62 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
 
             @test d == [d05, d04, d03]
             @test how == :successful_comparison
+
+            # Test folder structure
+            @test isfile(
+                joinpath(
+                    computed_dir,
+                    job_id,
+                    output,
+                    rfolder,
+                    "computed_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_01,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_02,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_03,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_04,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
+            @test isfile(
+                joinpath(
+                    save_dir,
+                    commit_sha_05,
+                    rfolder,
+                    job_id,
+                    "ref_prog_state.hdf5",
+                ),
+            )
         end
     end
 
@@ -1246,7 +1471,12 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
                 Spaces.ExtrudedFiniteDifferenceSpace(grid, Grids.CellCenter())
             comms_ctx = ClimaComms.context(space)
 
+            # Folder structure:
             job_id = "unit_test_export_reproducibility_results"
+            rfolder = "rbundle"
+            output = "output_active"
+            repro_dir = joinpath(computed_dir, job_id, output, rfolder)
+            mkpath(repro_dir)
 
             fv = Fields.FieldVector(; x = ones(space), y = ones(space))
 
@@ -1283,25 +1513,55 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
             @test isempty(dirs)
 
             # Successful comparisons, legacy path configuration
-            d01 = make_ref_file_counter(1, save_dir, "01")
-            d02 = make_ref_file_counter(2, save_dir, "02")
-            d03 = make_ref_file_counter(3, save_dir, "03")
-            d04 = make_ref_file_counter(3, save_dir, "04")
-            d05 = make_ref_file_counter(3, save_dir, "05")
-
-            put_data_file(d01, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d02, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d03, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d04, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            commit_sha_01 = "commit_hash_01"
+            commit_sha_02 = "commit_hash_02"
+            commit_sha_03 = "commit_hash_03"
+            commit_sha_04 = "commit_hash_04"
+            commit_sha_05 = "commit_hash_05"
+            d01 = make_ref_file_counter(1, save_dir, commit_sha_01)
+            d02 = make_ref_file_counter(2, save_dir, commit_sha_02)
+            d03 = make_ref_file_counter(3, save_dir, commit_sha_03)
+            d04 = make_ref_file_counter(3, save_dir, commit_sha_04)
+            d05 = make_ref_file_counter(3, save_dir, commit_sha_05)
+
+            put_data_file(
+                joinpath(d01, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d02, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d03, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d04, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
             fv.x .= 200
             fv.y .= 300
-            put_data_file(d05, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            put_data_file(
+                joinpath(d05, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
 
-            @test isfile(joinpath(d01, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d02, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d03, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d04, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d05, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d01, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d02, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d03, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d04, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d05, job_id, "ref_prog_state.hdf5"))
             @test isfile(joinpath(d01, "ref_counter.jl"))
             @test isfile(joinpath(d02, "ref_counter.jl"))
             @test isfile(joinpath(d03, "ref_counter.jl"))
@@ -1341,7 +1601,12 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
                 Spaces.ExtrudedFiniteDifferenceSpace(grid, Grids.CellCenter())
             comms_ctx = ClimaComms.context(space)
 
+            # Folder structure:
             job_id = "unit_test_export_reproducibility_results"
+            rfolder = "rbundle"
+            output = "output_active"
+            repro_dir = joinpath(computed_dir, job_id, output, rfolder)
+            mkpath(repro_dir)
 
             fv = Fields.FieldVector(; x = ones(space), y = ones(space))
 
@@ -1359,6 +1624,7 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
                     n = 10,
                     ref_counter_PR = 1,
                     skip = true,
+                    repro_folder = rfolder,
                 )
             @test how == :skipped
             @test isempty(dirs)
@@ -1377,30 +1643,61 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
                     n = 10,
                     ref_counter_PR = 1,
                     skip = false,
+                    repro_folder = rfolder,
                 )
             @test how == :no_comparable_dirs
             @test isempty(dirs)
 
-            # Successful comparisons, legacy path configuration
-            d01 = make_ref_file_counter(1, save_dir, rbundle("CH01"))
-            d02 = make_ref_file_counter(2, save_dir, rbundle("CH02"))
-            d03 = make_ref_file_counter(3, save_dir, rbundle("CH03"))
-            d04 = make_ref_file_counter(3, save_dir, rbundle("CH04"))
-            d05 = make_ref_file_counter(3, save_dir, rbundle("CH05"))
-
-            put_data_file(d01, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d02, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d03, fv, comms_ctx; filename = "ref_prog_state.hdf5")
-            put_data_file(d04, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            # Successful comparisons, legacy path configuration (no repro folder)
+            commit_sha_01 = "sha_01"
+            commit_sha_02 = "sha_02"
+            commit_sha_03 = "sha_03"
+            commit_sha_04 = "sha_04"
+            commit_sha_05 = "sha_05"
+            d01 = make_ref_file_counter(1, save_dir, commit_sha_01)
+            d02 = make_ref_file_counter(2, save_dir, commit_sha_02)
+            d03 = make_ref_file_counter(3, save_dir, commit_sha_03)
+            d04 = make_ref_file_counter(3, save_dir, commit_sha_04)
+            d05 = make_ref_file_counter(3, save_dir, commit_sha_05)
+
+            put_data_file(
+                joinpath(d01, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d02, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d03, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
+            put_data_file(
+                joinpath(d04, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
             fv.x .= 200
             fv.y .= 300
-            put_data_file(d05, fv, comms_ctx; filename = "ref_prog_state.hdf5")
+            put_data_file(
+                joinpath(d05, job_id),
+                fv,
+                comms_ctx;
+                filename = "ref_prog_state.hdf5",
+            )
 
-            @test isfile(joinpath(d01, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d02, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d03, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d04, "ref_prog_state.hdf5"))
-            @test isfile(joinpath(d05, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d01, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d02, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d03, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d04, job_id, "ref_prog_state.hdf5"))
+            @test isfile(joinpath(d05, job_id, "ref_prog_state.hdf5"))
             @test isfile(joinpath(d01, "ref_counter.jl"))
             @test isfile(joinpath(d02, "ref_counter.jl"))
             @test isfile(joinpath(d03, "ref_counter.jl"))
@@ -1420,14 +1717,21 @@ if pkgversion(ClimaCore) ≥ v"0.14.18"
                     n = 10,
                     ref_counter_PR = 3,
                     skip = false,
+                    repro_folder = rfolder,
                 )
             @test how == :successful_comparison
             @test dirs == [d05, d04, d03]
-            repro_dir = joinpath(computed_dir, "reproducibility_bundle")
+            repro_dir = joinpath(computed_dir, rfolder)
             @test isfile(joinpath(repro_dir, "computed_prog_state.hdf5"))
-            @test isfile(joinpath(repro_dir, "computed_mse_CH05.json"))
-            @test isfile(joinpath(repro_dir, "computed_mse_CH04.json"))
-            @test isfile(joinpath(repro_dir, "computed_mse_CH03.json"))
+            @test isfile(
+                joinpath(repro_dir, "computed_mse_$commit_sha_05.json"),
+            )
+            @test isfile(
+                joinpath(repro_dir, "computed_mse_$commit_sha_04.json"),
+            )
+            @test isfile(
+                joinpath(repro_dir, "computed_mse_$commit_sha_03.json"),
+            )
         end
     end
 end