diff --git a/.github/workflows/run.yml b/.github/workflows/run.yml
index bb5e1d3a0..83edafdf1 100644
--- a/.github/workflows/run.yml
+++ b/.github/workflows/run.yml
@@ -222,10 +222,10 @@ jobs:
           pip install -r ./requirements.txt
       - name: Run
         run: |-
-          output=$(./bin/benchpark configure --bootstrap-location . && ./bin/benchpark bootstrap 2>&1)
+          output=$(./bin/benchpark configure --bootstrap-location ./bootstrap && ./bin/benchpark bootstrap 2>&1)
 
           # 1. Check the path is present
-          echo "$output" | grep -q "/home/runner/work/benchpark/benchpark/.benchpark/ramble" \
+          echo "$output" | grep -q "/home/runner/work/benchpark/benchpark/bootstrap/ramble" \
             || { echo "Expected path not found"; exit 1; }
 
           # 2. Check "Cloning Ramble" appears exactly once
diff --git a/config/bootstrap.yaml b/config/bootstrap.yaml
new file mode 100644
index 000000000..4211d0e9e
--- /dev/null
+++ b/config/bootstrap.yaml
@@ -0,0 +1,6 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+bootstrap:
+  location: ~/.benchpark/
diff --git a/config/repos.yaml b/config/repos.yaml
new file mode 100644
index 000000000..2dffe1aeb
--- /dev/null
+++ b/config/repos.yaml
@@ -0,0 +1,9 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+repos:
+  experiments: [../experiments, ../experiments/test]
+  systems: [../systems]
+  applications: [../repo]
+  packages: [../repo]
diff --git a/docs/configuration.rst b/docs/configuration.rst
new file mode 100644
index 000000000..54312256b
--- /dev/null
+++ b/docs/configuration.rst
@@ -0,0 +1,68 @@
+..
+    Copyright 2023 Lawrence Livermore National Security, LLC and other
+    Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+
+    SPDX-License-Identifier: Apache-2.0
+
+#######################
+ Configuring Benchpark
+#######################
+
+Benchpark offers several options to configure usage. This includes:
+
+1. Configuring the location of the bootstrap directory (default is ``~/.benchpark``).
+   This is useful to change from the default value if you do not have much space in your
+   home directory, as the bootstrap contains the ``spack``, ``spack-packages``, and
+   ``ramble`` repositories.
+
+1. Configuring which repositories benchpark uses for objects in the
+   ``experiments/systems/repos`` directories (``experiment.py``, ``system.py``,
+   ``package.py``, and ``application.py``).
+
+**********************************************
+ Configuring the Benchpark Bootstrap Location
+**********************************************
+
+Benchpark clones ``ramble``, ``spack``, and ``spack-packages`` into a centralized
+location (by default this is ``~/.benchpark``) to enable building and running
+benchmarks. Benchpark workspaces copy over these repositories from the centralized
+location to avoid downloading from the internet when initializing a Benchpark workspace.
+The bootstrap location can be configured in ``<benchpark_root>/config/bootstrap.yaml``
+or by running ``benchpark configure --bootstrap-location <location>``.
+
+***********************************************
+ Configuring Which Repositories Benchpark Uses
+***********************************************
+
+The ``<benchpark_root>/config/repos.yaml`` file is used to fully customize ``system``
+and ``experiment`` repositories used by Benchpark, ``application`` repositories used by
+Ramble, and package repositories used by Spack. For Spack and Ramble, the builtin
+repository is always used (in addition to whatever package repositories are specified).
+The order in which repositories appear in ``<benchpark_root>/config/repos.yaml`` will
+determine their precedence, so if you desire to use a custom repository, it should be
+listed before any other repositories.
+
+**********************************************************************
+ Automatically Generating Configurations with ``benchpark configure``
+**********************************************************************
+
+``benchpark configure`` is designed to create the ``yaml`` configurations for you. As of
+now, it can only generate bootstrap config (``bootstrap.yaml``). If no bootstrap config
+is detected in the chosen scope, this will auto-generate it. ``benchpark configure``
+cannot generate a ``repos.yaml`` file at the moment, this must be written manually.
+
+**********************
+ Configuration Scopes
+**********************
+
+Benchpark can pull configurations from one location, with the following priority
+(highest first):
+
+- As an argument to ``benchpark``: ``benchpark -C <dir>...``
+- If the CWD where you invoke the benchpark executable has ``benchpark-config``
+  directory
+- If ``<benchpark_root>/config`` is a directory; this must exist if the first two don't
+
+There is no mixing and matching between these tiers. If you are using ``-C``, then the
+specified directory must contain a ``bootstrap.yaml`` and a ``repos.yaml`` (you can copy
+from ``<benchpark_root>/config`` if you want the same config).
diff --git a/docs/generate-benchmark-list.py b/docs/generate-benchmark-list.py
index f6bc005be..852bd0252 100755
--- a/docs/generate-benchmark-list.py
+++ b/docs/generate-benchmark-list.py
@@ -8,7 +8,6 @@
 
 sys.path.append("../lib/")
 import benchpark.accounting  # noqa: E402
-import benchpark.paths  # noqa: E402
 
 
 def construct_tag_groups(tag_groups, tag_dicts, dictionary):
diff --git a/docs/index.rst b/docs/index.rst
index 03c879b84..afdd5147e 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -40,6 +40,7 @@
     run-experiment
     analyze-experiment
     benchpark-analyze
+    configuration
     modifiers
     set-of-experiments
     run-binary
diff --git a/experiments/test/repo.yaml b/experiments/test/repo.yaml
new file mode 100644
index 000000000..6f321df87
--- /dev/null
+++ b/experiments/test/repo.yaml
@@ -0,0 +1,7 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+repo:
+  namespace: test
+  subdirectory: ''
diff --git a/experiments/saxpy/experiment.py b/experiments/test/saxpy/experiment.py
similarity index 100%
rename from experiments/saxpy/experiment.py
rename to experiments/test/saxpy/experiment.py
diff --git a/lib/benchpark/accounting.py b/lib/benchpark/accounting.py
index eb31c5a7c..e8a289fee 100644
--- a/lib/benchpark/accounting.py
+++ b/lib/benchpark/accounting.py
@@ -6,7 +6,7 @@
 import os
 from collections import defaultdict
 
-import benchpark.paths
+from benchpark.base_paths import base_paths
 
 PROGRAMMING_MODEL_CATEGORY = "programming_model"
 SCALING_CATEGORY = "scaling"
@@ -30,7 +30,7 @@
 
 
 def benchpark_experiments(exp_dict=EXP_DICT, exclude_variants=[]):
-    source_dir = benchpark.paths.benchpark_root
+    source_dir = base_paths.benchpark_root
     experiments = []
     experiments_dir = source_dir / "experiments"
 
@@ -60,7 +60,7 @@ def benchpark_experiments(exp_dict=EXP_DICT, exclude_variants=[]):
 
 def benchpark_modifiers():
     all_benchmark_modifiers = ["affinity", "allocation", "hwloc"]
-    source_dir = benchpark.paths.benchpark_root
+    source_dir = base_paths.benchpark_root
     experiments_dir = source_dir / "experiments"
     modifiers = []
     exclude = ["modifier_repo.yaml"]
@@ -88,7 +88,7 @@ def benchpark_modifiers():
 def benchpark_systems(programming_model=None):
     from benchpark.spec import SystemSpec
 
-    source_dir = benchpark.paths.benchpark_root
+    source_dir = base_paths.benchpark_root
     systems = []
     exclude = ["all_hardware_descriptions", "common", "repo.yaml"]
     for x in sorted(os.listdir(source_dir / "systems")):
@@ -128,7 +128,7 @@ def benchpark_systems(programming_model=None):
 
 
 def benchpark_benchmarks():
-    source_dir = benchpark.paths.benchpark_root
+    source_dir = base_paths.benchpark_root
     benchmarks = []
     experiments_dir = source_dir / "experiments"
     for x in sorted(os.listdir(experiments_dir)):
diff --git a/lib/benchpark/base_paths.py b/lib/benchpark/base_paths.py
new file mode 100644
index 000000000..0ce4010de
--- /dev/null
+++ b/lib/benchpark/base_paths.py
@@ -0,0 +1,56 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import pathlib
+
+
+def _source_location() -> pathlib.Path:
+    """Return the location of the project source files directory."""
+    path_to_this_file = __file__
+    return pathlib.Path(path_to_this_file).resolve().parents[2]
+
+
+_unset = object()
+
+
+class BasePaths:
+    def __init__(self):
+        self.benchpark_root = _source_location()
+        self.lib_path = self.benchpark_root / "lib" / "benchpark"
+        self.test_path = self.lib_path / "test"
+        self.hardware_descriptions = (
+            self.benchpark_root / "systems" / "all_hardware_descriptions"
+        )
+        self.checkout_versions = self.benchpark_root / "checkout-versions.yaml"
+        self.remote_urls = self.benchpark_root / "remote-urls.yaml"
+        self.invocation_working_dir = None
+        self.user_input_cfg = _unset
+
+
+base_paths = BasePaths()
+
+
+def determine_config_dir():
+    """
+    Benchpark configs don't merge or override like Spack/Ramble. You
+    just point it at a directory and that's where all your config is.
+    """
+    if base_paths.user_input_cfg is _unset:
+        raise Exception("Internal error: config initialization")
+    elif base_paths.user_input_cfg:
+        if not base_paths.user_input_cfg.exists():
+            raise Exception(
+                f"Specific config dir does not exist: {base_paths.user_input_cfg}"
+            )
+        else:
+            return base_paths.user_input_cfg
+
+    possible_dirs = [
+        base_paths.invocation_working_dir / "benchpark-config",
+        base_paths.benchpark_root / "config",
+    ]
+    for pd in possible_dirs:
+        if pd.exists():
+            return pd
diff --git a/lib/benchpark/cmd/configure.py b/lib/benchpark/cmd/configure.py
index 4020b07d0..6a1ccac5d 100644
--- a/lib/benchpark/cmd/configure.py
+++ b/lib/benchpark/cmd/configure.py
@@ -8,7 +8,7 @@
 
 import yaml
 
-import benchpark.paths
+import benchpark.config
 
 
 def setup_parser(root_parser):
@@ -21,15 +21,14 @@ def setup_parser(root_parser):
 
 
 def command(args):
-    data = {}
-
-    if args.bootstrap_location:
-        loc = os.path.expandvars(os.path.expanduser(args.bootstrap_location))
-        bl = str(Path(loc).resolve()).rstrip("/") + "/.benchpark/"
-        data["bootstrap"] = {
-            "location": bl,
-        }
-
-    print(f"Writing configuration to {benchpark.paths.benchpark_config}")
-    with open(benchpark.paths.benchpark_config, "w") as yaml_file:
-        yaml.safe_dump(data, yaml_file)
+    bootstrap_cfg = benchpark.config.configuration().bootstrap
+
+    if args.bootstrap_location or not bootstrap_cfg.path.exists():
+        where = args.bootstrap_location or "~/.benchpark/"
+        loc = os.path.expandvars(os.path.expanduser(where))
+        bl = str(Path(loc).resolve()).rstrip("/")
+        data = {"bootstrap": {"location": bl}}
+
+        print(f"Writing configuration to {bootstrap_cfg.path}")
+        with open(bootstrap_cfg.path, "w") as yaml_file:
+            yaml.safe_dump(data, yaml_file)
diff --git a/lib/benchpark/cmd/info.py b/lib/benchpark/cmd/info.py
index f4dc847fd..8be1963f8 100644
--- a/lib/benchpark/cmd/info.py
+++ b/lib/benchpark/cmd/info.py
@@ -5,7 +5,8 @@
 import llnl.util.tty.color as color
 import yaml
 
-import benchpark.paths
+import benchpark.spec
+from benchpark.paths import paths
 
 
 def indent():
@@ -71,7 +72,7 @@ def _handle_query(query):
         key, value = query.split("=", 1)
         exclude = {"all_hardware_descriptions", "repo.yaml", "generic-x86"}
         all_system_specs = []
-        for d in set(os.listdir(benchpark.paths.benchpark_root / "systems")) - exclude:
+        for d in set(os.listdir(paths.benchpark_root / "systems")) - exclude:
             all_system_specs.append(benchpark.spec.SystemSpec(d))
 
         matching_systems = []
diff --git a/lib/benchpark/cmd/mirror.py b/lib/benchpark/cmd/mirror.py
index 0e77b3de8..ef3d66988 100644
--- a/lib/benchpark/cmd/mirror.py
+++ b/lib/benchpark/cmd/mirror.py
@@ -12,7 +12,7 @@
 import shutil
 import tempfile
 
-import benchpark.paths
+from benchpark.paths import paths
 from benchpark.runtime import run_command, working_dir
 
 
@@ -115,7 +115,7 @@ def mirror_create(args):
         )
 
     cache_storage = os.path.join(dest, "pip-cache")
-    ramble_pip_reqs = os.path.join(benchpark.paths.benchpark_root, "requirements.txt")
+    ramble_pip_reqs = os.path.join(paths.benchpark_root, "requirements.txt")
     if not os.path.exists(cache_storage):
         run_command(f"pip download -r {ramble_pip_reqs} -d {cache_storage}")
 
@@ -159,7 +159,7 @@ def _ignore(path, dir_list):
     env_dir = os.path.dirname(find_one(ramble_workspace, "spack.yaml"))
     git_repo_dst = os.path.join(dest, "git-repos")
     repo_copy_script = os.path.join(
-        benchpark.paths.benchpark_root, "lib", "scripts", "env-collect-branch-tips.py"
+        paths.benchpark_root, "lib", "scripts", "env-collect-branch-tips.py"
     )
     out, err = run_command(
         f"spack -e {env_dir} python {repo_copy_script} {git_repo_dst}"
@@ -199,12 +199,12 @@ def _ignore(path, dir_list):
 """)
 
     modifiers_dest = os.path.join(dest, "modifiers")
-    modifiers_src = os.path.join(benchpark.paths.benchpark_root, "modifiers")
+    modifiers_src = os.path.join(paths.benchpark_root, "modifiers")
     if not os.path.exists(modifiers_dest):
         shutil.copytree(modifiers_src, modifiers_dest)
 
     bp_repo_dest = os.path.join(dest, "repo")
-    bp_repo_src = os.path.join(benchpark.paths.benchpark_root, "repo")
+    bp_repo_src = os.path.join(paths.benchpark_root, "repo")
     if not os.path.exists(bp_repo_dest):
         shutil.copytree(bp_repo_src, bp_repo_dest)
 
diff --git a/lib/benchpark/cmd/setup.py b/lib/benchpark/cmd/setup.py
index aaa9ba024..fdfa82f6f 100644
--- a/lib/benchpark/cmd/setup.py
+++ b/lib/benchpark/cmd/setup.py
@@ -12,8 +12,9 @@
 
 import ruamel.yaml as yaml
 
-import benchpark.paths
+import benchpark.config
 from benchpark.debug import debug_print
+from benchpark.paths import paths
 from benchpark.runtime import RuntimeResources
 
 
@@ -95,7 +96,7 @@ def _find(d, tag):
                     return result
 
     experiments_root = pathlib.Path(os.path.abspath(args.experiments_root))
-    source_dir = benchpark.paths.benchpark_root
+    source_dir = paths.benchpark_root
 
     experiment_src_dir = pathlib.Path(os.path.abspath(str(args.experiment)))
 
@@ -200,9 +201,11 @@ def include_fn(fname):
     run_script = experiments_root / ".latest-experiment.sh"
 
     per_workspace_setup = RuntimeResources(
-        experiments_root, upstream=RuntimeResources(benchpark.paths.benchpark_home)
+        experiments_root, upstream=RuntimeResources(paths.benchpark_home)
     )
 
+    repos_cfg = benchpark.config.configuration().repos
+
     pkg_str = ""
     if pkg_manager == "spack":
         spack_build_stage = experiments_root / "builds"
@@ -212,12 +215,18 @@ def include_fn(fname):
             site_repos = (
                 per_workspace_setup.spack_location / "etc" / "spack" / "repos.yaml"
             )
+            repos = {}
+            for repo_dir in reversed(repos_cfg.packages):
+                repo_dir = repos_cfg.resolve_path(repo_dir)
+                with open(repo_dir / "repo.yaml", "r") as f:
+                    repo_data = yaml.safe_load(f)
+                    namespace = repo_data["repo"]["namespace"]
+                    repos[namespace] = str(repo_dir)
+            repos["builtin"] = (
+                f"{per_workspace_setup.pkgs_location}/repos/spack_repo/builtin/"
+            )
             with open(site_repos, "w") as f:
-                f.write(f"""\
-repos::
-  benchpark: {source_dir}/repo
-  builtin: {per_workspace_setup.pkgs_location}/repos/spack_repo/builtin/
-""")
+                yaml.dump({"repos:": repos}, f, default_flow_style=False)
             spack(
                 f"config --scope=site add \"config:build_stage:['{spack_build_stage}']\""
             )
@@ -230,7 +239,9 @@ def include_fn(fname):
 
     ramble, first_time_ramble = per_workspace_setup.ramble_first_time_setup()
     if first_time_ramble:
-        ramble(f"repo add --scope=site {source_dir}/repo")
+        for repo_dir in reversed(repos_cfg.applications):
+            repo_dir = repos_cfg.resolve_path(repo_dir)
+            ramble(f"repo add --scope=site {repo_dir}")
         ramble('config --scope=site add "config:disable_progress_bar:true"')
         ramble(f"repo add -t modifiers --scope=site {source_dir}/modifiers")
         ramble("config --scope=site add \"config:spack:global:args:'-d'\"")
diff --git a/lib/benchpark/cmd/show_build.py b/lib/benchpark/cmd/show_build.py
index fdb947a48..40649e09d 100644
--- a/lib/benchpark/cmd/show_build.py
+++ b/lib/benchpark/cmd/show_build.py
@@ -11,7 +11,7 @@
 import re
 import shutil
 
-import benchpark.paths
+from benchpark.paths import paths
 from benchpark.runtime import run_command
 
 
@@ -48,7 +48,7 @@ def show_build_dump(args):
     env_root = _find_env_root(args.workspace)
 
     determine_exp = os.path.join(
-        benchpark.paths.benchpark_root, "lib", "scripts", "experiment-build-info.py"
+        paths.benchpark_root, "lib", "scripts", "experiment-build-info.py"
     )
     out, err = run_command(f"spack -e {env_root} python {determine_exp}")
     exp_info = json.loads(out)
diff --git a/lib/benchpark/cmd/system.py b/lib/benchpark/cmd/system.py
index ac1e60f31..7549b6d4f 100644
--- a/lib/benchpark/cmd/system.py
+++ b/lib/benchpark/cmd/system.py
@@ -16,9 +16,9 @@
 import yaml
 from deepdiff import DeepDiff
 
-import benchpark.paths
 import benchpark.spec
 import benchpark.system
+from benchpark.paths import paths
 
 
 def system_init(args):
@@ -63,16 +63,14 @@ def system_external(args):
     if args.new_system:
         subprocess.run(
             [
-                benchpark.paths.benchpark_home / "spack/bin/spack",
+                paths.benchpark_home / "spack/bin/spack",
                 "external",
                 "find",
                 "--not-buildable",
             ]
         )
 
-        with open(
-            benchpark.paths.benchpark_home / "spack/etc/spack/packages.yaml", "r"
-        ) as file:
+        with open(paths.benchpark_home / "spack/etc/spack/packages.yaml", "r") as file:
             new_packages = yaml.safe_load(file)["packages"]
 
         color.cprint("@*rHere are all of the new packages:@.")
@@ -86,7 +84,7 @@ def system_external(args):
     pkg_list = list(packages.keys())
     subprocess.run(
         [
-            benchpark.paths.benchpark_home / "spack/bin/spack",
+            paths.benchpark_home / "spack/bin/spack",
             "external",
             "find",
             "--not-buildable",
@@ -94,9 +92,7 @@ def system_external(args):
         + [pkg for pkg in pkg_list]
     )
 
-    with open(
-        benchpark.paths.benchpark_home / "spack/etc/spack/packages.yaml", "r"
-    ) as file:
+    with open(paths.benchpark_home / "spack/etc/spack/packages.yaml", "r") as file:
         new_packages = yaml.safe_load(file)["packages"]
 
     # Use DeepDiff to find differences
diff --git a/lib/benchpark/cmd/unit_test.py b/lib/benchpark/cmd/unit_test.py
index 5e1ecc241..e01a5c086 100644
--- a/lib/benchpark/cmd/unit_test.py
+++ b/lib/benchpark/cmd/unit_test.py
@@ -14,7 +14,7 @@
 import llnl.util.tty.color as color
 import pytest
 
-import benchpark.paths
+from benchpark.paths import paths
 
 
 def setup_parser(subparser):
@@ -111,10 +111,10 @@ def colorize(c, prefix):
     # which doesn't need to wait for pytest collection and doesn't
     # require parsing pytest output
     files = llnl.util.filesystem.find(
-        root=benchpark.paths.test_path, files="*.py", recursive=True
+        root=paths.test_path, files="*.py", recursive=True
     )
     files = [
-        os.path.relpath(f, start=benchpark.paths.benchpark_root)
+        os.path.relpath(f, start=paths.benchpark_root)
         for f in files
         if not f.endswith(("conftest.py", "__init__.py"))
     ]
@@ -145,7 +145,7 @@ def colorize(c, prefix):
 
         len_indent = len(indent)
         if os.path.isabs(name):
-            name = os.path.relpath(name, start=benchpark.paths.benchpark_root)
+            name = os.path.relpath(name, start=paths.benchpark_root)
 
         item = (len_indent, name, nodetype)
 
@@ -212,7 +212,7 @@ def command(args, unknown_args):
 
     # add back any parsed pytest args we need to pass to pytest
     pytest_args = add_back_pytest_args(args, unknown_args)
-    pytest_root = benchpark.paths.benchpark_root
+    pytest_root = paths.benchpark_root
 
     if args.numprocesses is not None and args.numprocesses > 1:
         pytest_args.extend(
diff --git a/lib/benchpark/config.py b/lib/benchpark/config.py
new file mode 100644
index 000000000..86fcda30e
--- /dev/null
+++ b/lib/benchpark/config.py
@@ -0,0 +1,102 @@
+# Copyright 2023 Lawrence Livermore National Security, LLC and other
+# Benchpark Project Developers. See the top-level COPYRIGHT file for details.
+#
+# Copyright 2022-2024 The Ramble Authors
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import pathlib
+
+import yaml
+
+import benchpark.base_paths
+
+
+class RequiredClassAttr:
+    def __init__(self, name):
+        self.name = name
+
+    def __get__(self, obj, owner):
+        raise NotImplementedError(
+            f"{owner.__name__} must define class attribute '{self.name}'"
+        )
+
+
+class PropertyDict:
+    def __getattr__(self, name):
+        val = self.data[name]
+        if isinstance(val, dict):
+            return PropertyDict(val)
+        return val
+
+
+class ConfigSection(PropertyDict):
+    def __init__(self, data, path):
+        self.data = data
+        self.path = pathlib.Path(path)
+
+    filename = RequiredClassAttr("filename")
+    name = RequiredClassAttr("name")
+
+    @classmethod
+    def try_load(cls, cfg_dir):
+        cfg_path = pathlib.Path(cfg_dir) / cls.filename
+        if cfg_path.exists():
+            with open(cfg_path, "r") as f:
+                data = yaml.safe_load(f)[cls.name]
+        else:
+            data = {}
+        return cls(data, cfg_path)
+
+    def resolve_path(self, value):
+        path = pathlib.Path(value)
+        if not path.is_absolute():
+            return (self.path.parents[0] / path).resolve()
+
+    def __getattr__(self, name):
+        if not self.data:
+            raise Exception(f"Missing config in {self.path}")
+        return super().__getattr__(name)
+
+
+class Repos(ConfigSection):
+    filename = "repos.yaml"
+    name = "repos"
+
+
+class Bootstrap(ConfigSection):
+    filename = "bootstrap.yaml"
+    name = "bootstrap"
+
+
+_section_types = [Repos, Bootstrap]
+
+
+class Configuration:
+    section_names = [st.name for st in _section_types]
+
+    def __init__(self, cfg_dir):
+        self.sections = {}
+        for st in _section_types:
+            attempt = st.try_load(cfg_dir)
+            if attempt:
+                self.sections[st.name] = attempt
+
+    def __getattr__(self, name):
+        if name in self.sections:
+            return self.sections[name]
+        elif name in Configuration.section_names:
+            raise Exception("This section is not present in this config")
+        else:
+            raise AttributeError("No such section")
+
+
+_configuration = None
+
+
+def configuration():
+    global _configuration
+    if not _configuration:
+        _configuration = Configuration(benchpark.base_paths.determine_config_dir())
+
+    return _configuration
diff --git a/lib/benchpark/directives.py b/lib/benchpark/directives.py
index 405c841bf..3965fea55 100644
--- a/lib/benchpark/directives.py
+++ b/lib/benchpark/directives.py
@@ -18,7 +18,6 @@
 import ramble.language.shared_language
 from ramble.language.language_base import DirectiveError
 
-import benchpark.paths
 import benchpark.repo
 import benchpark.runtime
 import benchpark.spec
diff --git a/lib/benchpark/paths.py b/lib/benchpark/paths.py
index b172d72c6..467cf9f2f 100644
--- a/lib/benchpark/paths.py
+++ b/lib/benchpark/paths.py
@@ -6,32 +6,23 @@
 import os
 import pathlib
 
-import yaml
+import benchpark.base_paths
+import benchpark.config
 
 
-def _source_location() -> pathlib.Path:
-    """Return the location of the project source files directory."""
-    path_to_this_file = __file__
-    return pathlib.Path(path_to_this_file).resolve().parents[2]
+class Paths:
+    def __init__(self, base_paths):
+        bootstrap_cfg = benchpark.config.configuration().bootstrap
 
+        self.benchpark_home = pathlib.Path(os.path.expanduser(bootstrap_cfg.location))
+        self.global_ramble_path = self.benchpark_home / "ramble"
+        self.global_spack_path = self.benchpark_home / "spack"
 
-benchpark_root = _source_location()
-lib_path = benchpark_root / "lib" / "benchpark"
-test_path = lib_path / "test"
+        self.base_paths = base_paths
 
-benchpark_config = benchpark_root / "configure.yaml"
+    def __getattr__(self, name):
+        return getattr(self.base_paths, name)
 
-if benchpark_config.exists():
-    with benchpark_config.open("r") as f:
-        config = yaml.safe_load(f)
-        benchpark_home = config["bootstrap"]["location"]
-else:
-    benchpark_home = "~/.benchpark"
-benchpark_home = pathlib.Path(os.path.expanduser(benchpark_home))
 
-
-global_ramble_path = benchpark_home / "ramble"
-global_spack_path = benchpark_home / "spack"
-hardware_descriptions = benchpark_root / "systems" / "all_hardware_descriptions"
-checkout_versions = benchpark_root / "checkout-versions.yaml"
-remote_urls = benchpark_root / "remote-urls.yaml"
+paths = Paths(benchpark.base_paths.base_paths)
+hardware_descriptions = paths.hardware_descriptions
diff --git a/lib/benchpark/repo.py b/lib/benchpark/repo.py
index ffff86b1f..72473e8b1 100644
--- a/lib/benchpark/repo.py
+++ b/lib/benchpark/repo.py
@@ -9,7 +9,7 @@
 import sys
 from enum import Enum
 
-import benchpark.paths
+import benchpark.config
 
 # isort: off
 
@@ -74,23 +74,8 @@ def override_ramble_hardcoded_globals():
     ramble.language.language_base.namespaces = _old[2]
 
 
-# Experiments
-def _exprs():
-    """Get the singleton RepoPath instance for Ramble.
-
-    Create a RepoPath, add it to sys.meta_path, and return it.
-
-    TODO: consider not making this a singleton.
-    """
-    experiments_repo = benchpark.paths.benchpark_root / "experiments"
-    return _add_repo(experiments_repo, ObjectTypes.experiments)
-
-
-def _add_repo(repo_dir, obj_type):
-    if repo_dir.exists():
-        repo_dirs = [str(repo_dir)]
-    else:
-        raise ValueError(f"Repo dir does not exist: {repo_dir}")
+def _add_repo(repo_dirs, obj_type):
+    repo_dirs = [str(x) for x in repo_dirs]
 
     with override_ramble_hardcoded_globals():
         path = ramble.repository.RepoPath(*repo_dirs, object_type=obj_type)
@@ -98,10 +83,16 @@ def _add_repo(repo_dir, obj_type):
     return path
 
 
-# Systems
+def _exprs():
+    cfg = benchpark.config.configuration().repos
+    exp_repos = [cfg.resolve_path(x) for x in cfg.experiments]
+    return _add_repo(exp_repos, ObjectTypes.experiments)
+
+
 def _systems():
-    systems_repo = benchpark.paths.benchpark_root / "systems"
-    return _add_repo(systems_repo, ObjectTypes.systems)
+    cfg = benchpark.config.configuration().repos
+    sys_repos = [cfg.resolve_path(x) for x in cfg.systems]
+    return _add_repo(sys_repos, ObjectTypes.systems)
 
 
 paths = {
diff --git a/lib/benchpark/runtime.py b/lib/benchpark/runtime.py
index 7866a4bb8..69b47fe36 100644
--- a/lib/benchpark/runtime.py
+++ b/lib/benchpark/runtime.py
@@ -12,8 +12,8 @@
 
 import yaml
 
-import benchpark.paths
 from benchpark.debug import debug_print
+from benchpark.paths import paths
 
 
 @contextmanager
@@ -75,7 +75,7 @@ def __init__(self, dest, upstream=None):
         )
 
         # Read pinned versions of ramble and spack
-        with open(benchpark.paths.checkout_versions, "r") as yaml_file:
+        with open(paths.checkout_versions, "r") as yaml_file:
             data = yaml.safe_load(yaml_file)["versions"]
             self.ramble_commit, self.spack_commit, self.pkgs_commit = (
                 data["ramble"],
@@ -84,7 +84,7 @@ def __init__(self, dest, upstream=None):
             )
 
         # Read remote urls for ramble and spack
-        with open(benchpark.paths.remote_urls, "r") as yaml_file:
+        with open(paths.remote_urls, "r") as yaml_file:
             data = yaml.safe_load(yaml_file)["urls"]
             remote_ramble_url, remote_spack_url, remote_pkgs_url = (
                 data["ramble"],
diff --git a/lib/benchpark/test/caliper.py b/lib/benchpark/test/caliper.py
index 7aca10d05..bfab95663 100644
--- a/lib/benchpark/test/caliper.py
+++ b/lib/benchpark/test/caliper.py
@@ -10,8 +10,8 @@
 from ramble.expander import Expander
 
 import benchpark.caliper
-import benchpark.paths
 import benchpark.spec
+from benchpark.paths import paths
 
 
 def get_caliper_vars_section(expr_spec):
@@ -58,7 +58,7 @@ def test_caliper_modifier(monkeypatch):
     expr_vars_section = get_caliper_vars_section(expr_spec)
 
     # Append path to enable import of modifier and application
-    sys.path.append(str(benchpark.paths.benchpark_root))
+    sys.path.append(str(paths.benchpark_root))
     from modifiers.caliper.modifier import Caliper as CaliperModifier
     from repo.saxpy.application import Saxpy
 
diff --git a/lib/benchpark/test/commands.py b/lib/benchpark/test/commands.py
index 50b3f9674..93bcbdf11 100644
--- a/lib/benchpark/test/commands.py
+++ b/lib/benchpark/test/commands.py
@@ -5,14 +5,14 @@
 
 import subprocess
 
-import benchpark.paths
+from benchpark.paths import paths
 
 
 def test_list():
     for subcmd in ["experiments", "modifiers", "systems", "benchmarks"]:
         # Test with title (default behavior)
         result_with_title = subprocess.run(
-            [benchpark.paths.benchpark_root / "bin/benchpark", "list", subcmd],
+            [paths.benchpark_root / "bin/benchpark", "list", subcmd],
             check=True,
             capture_output=True,
             text=True,
@@ -24,7 +24,7 @@ def test_list():
         # Test without title (--no-title flag)
         result_no_title = subprocess.run(
             [
-                benchpark.paths.benchpark_root / "bin/benchpark",
+                paths.benchpark_root / "bin/benchpark",
                 "list",
                 subcmd,
                 "--no-title",
@@ -46,7 +46,7 @@ def test_list():
     # Check filtering
     check_cuda = subprocess.run(
         [
-            benchpark.paths.benchpark_root / "bin/benchpark",
+            paths.benchpark_root / "bin/benchpark",
             "list",
             "experiments",
             "--experiment",
@@ -64,7 +64,7 @@ def test_list():
 
 def test_tags():
     subprocess.run(
-        [benchpark.paths.benchpark_root / "bin/benchpark", "tags", "-a", "ad"],
+        [paths.benchpark_root / "bin/benchpark", "tags", "-a", "ad"],
         check=True,
     )
 
@@ -72,7 +72,7 @@ def test_tags():
 def test_info():
     text = subprocess.run(
         [
-            benchpark.paths.benchpark_root / "bin/benchpark",
+            paths.benchpark_root / "bin/benchpark",
             "list",
             "systems",
             "--no-title",
@@ -89,7 +89,7 @@ def test_info():
 
     for r in result:
         subprocess.run(
-            [benchpark.paths.benchpark_root / "bin/benchpark", "info", "system", r],
+            [paths.benchpark_root / "bin/benchpark", "info", "system", r],
             check=True,
             capture_output=True,
         )
diff --git a/lib/benchpark/test/paths.py b/lib/benchpark/test/paths.py
index 862124ca0..79b651374 100644
--- a/lib/benchpark/test/paths.py
+++ b/lib/benchpark/test/paths.py
@@ -5,9 +5,9 @@
 
 import pathlib
 
-import benchpark.paths
+from benchpark.paths import paths
 
 
 def test_benchpark_root(pytestconfig):
     expected_path = pathlib.Path(pytestconfig.inipath).resolve().parent
-    assert benchpark.paths.benchpark_root == expected_path
+    assert paths.benchpark_root == expected_path
diff --git a/lib/main.py b/lib/main.py
index 7b37208be..95adde548 100755
--- a/lib/main.py
+++ b/lib/main.py
@@ -7,12 +7,16 @@
 
 import argparse
 import inspect
+import os
+import pathlib
 import shlex
 import subprocess
 import sys
 
 import yaml
 
+# Process --version/--help early and exit before doing any further imports
+# (which can result in expensive cloning operations).
 __version__ = "0.1.0"
 if "-V" in sys.argv or "--version" in sys.argv:
     print(__version__)
@@ -20,11 +24,9 @@
 helpstr = """usage: main.py [-h] [-V] {tags,system,experiment,setup,unit-test,audit,mirror,info,show-build,list,bootstrap,analyze,aggregate,configure} ...
 
 Benchpark
-
 options:
   -h, --help            show this help message and exit
   -V, --version         show version number and exit
-
 Subcommands:
   {tags,system,experiment,setup,unit-test,audit,mirror,info,show-build,list,bootstrap,analyze,aggregate,configure}
     tags                Tags in Benchpark experiments
@@ -39,6 +41,7 @@
     list                List experiments, systems, benchmarks, and modifiers
     bootstrap           Bootstrap benchpark or update an existing bootstrap
     analyze             Perform pre-defined analysis on the performance data (caliper files) after 'ramble on'
+    redo                Re-instantiate system and all associated experiments
     aggregate           Aggregate multiple experiments (even across workspaces) into the same submission script
     configure           Configure options relating to the Benchpark environment
     """
@@ -46,13 +49,36 @@
     print(helpstr)
     exit()
 
-import benchpark.paths  # noqa: E402
-from benchpark.runtime import RuntimeResources  # noqa: E402
+from benchpark.base_paths import base_paths  # noqa: E402
+
+# Set paths here that are important for configuration: after this block
+# commands that use config can be imported and run
+_found_cfg = False
+for i, arg in enumerate(sys.argv):
+    if arg.startswith("-C") or arg.startswith("--config"):
+        _found_cfg = True
+        if "=" in arg:
+            val = arg.split("=")[1]
+        else:
+            val = sys.argv[i + 1]
+        base_paths.user_input_cfg = pathlib.Path(val)
+if not _found_cfg:
+    base_paths.user_input_cfg = None
+
+base_paths.invocation_working_dir = pathlib.Path(os.getcwd()).absolute().resolve()
 
-if sys.argv[1] == "configure":
+# Later imports initiate bootstrapping, and the configure command may want
+# to configure this behavior, so we handle it before doing remaining imports
+if "configure" in sys.argv:
     import benchpark.cmd.configure  # noqa: E402
 
     parser = argparse.ArgumentParser(description="Benchpark")
+    parser.add_argument(
+        "-C",
+        "--config",
+        help="Use config related to system/experiment/workspace generation."
+        " Default is <benchpark_root>/config/",
+    )
     subparsers = parser.add_subparsers(title="Subcommands", dest="subcommand")
     configure_parser = subparsers.add_parser(
         "configure", help="Configure options relating to the Benchpark environment"
@@ -62,7 +88,10 @@
     benchpark.cmd.configure.command(args)
     sys.exit(0)
 
-bootstrapper = RuntimeResources(benchpark.paths.benchpark_home)  # noqa
+from benchpark.paths import paths  # noqa: E402
+from benchpark.runtime import RuntimeResources  # noqa: E402
+
+bootstrapper = RuntimeResources(paths.benchpark_home)  # noqa
 bootstrapper.bootstrap()  # noqa
 
 import benchpark.cmd.aggregate  # noqa: E402
@@ -95,6 +124,14 @@ def main():
     parser.add_argument(
         "-V", "--version", action="store_true", help="show version number and exit"
     )
+    # -C is actually processed above here, in the imports, but must
+    # be registered here because otherwise argparse will think there
+    # is an invalid option.
+    parser.add_argument(
+        "-C",
+        "--config",
+        help="use config related to system/experiment/workspace generation",
+    )
 
     subparsers = parser.add_subparsers(title="Subcommands", dest="subcommand")
 
@@ -143,7 +180,7 @@ def supports_unknown_args(command):
 
 
 def benchpark_get_tags():
-    f = benchpark.paths.benchpark_root / "taxonomy.yaml"
+    f = paths.benchpark_root / "taxonomy.yaml"
     tags = []
 
     with open(f, "r") as stream:
@@ -335,8 +372,8 @@ def benchpark_tags_handler(args):
     """
     Filter ramble tags by benchpark benchmarks
     """
-    source_dir = benchpark.paths.benchpark_root
-    ramble_exe = benchpark.paths.benchpark_home / "ramble/bin/ramble"
+    source_dir = paths.benchpark_root
+    ramble_exe = paths.benchpark_home / "ramble/bin/ramble"
     subprocess.run([ramble_exe, "repo", "add", "--scope=site", f"{source_dir}/repo"])
     benchmarks = benchpark_benchmarks()
 
diff --git a/lib/scripts/diffExperimentBuilds.py b/lib/scripts/diffExperimentBuilds.py
index 466387df1..83e898ced 100644
--- a/lib/scripts/diffExperimentBuilds.py
+++ b/lib/scripts/diffExperimentBuilds.py
@@ -4,9 +4,9 @@
 import subprocess
 import sys
 
-import benchpark.paths
+from benchpark.paths import paths
 
-sys.path.append(str(benchpark.paths.benchpark_home) + "/spack/lib/spack")
+sys.path.append(str(paths.benchpark_home) + "/spack/lib/spack")
 import llnl.util.tty.color as color  # noqa: E402
 
 
diff --git a/lib/scripts/diffExperimentSpecs.py b/lib/scripts/diffExperimentSpecs.py
index db6235913..a867733f2 100644
--- a/lib/scripts/diffExperimentSpecs.py
+++ b/lib/scripts/diffExperimentSpecs.py
@@ -5,9 +5,9 @@
 
 from diffSystems import compare_yaml
 
-import benchpark.paths
+from benchpark.paths import paths
 
-sys.path.append(str(benchpark.paths.benchpark_home) + "/spack/lib/spack")
+sys.path.append(str(paths.benchpark_home) + "/spack/lib/spack")
 import llnl.util.tty.color as color  # noqa: E402
 
 
diff --git a/lib/scripts/diffPackageCommits.py b/lib/scripts/diffPackageCommits.py
index 9d9a44b8a..376df0131 100644
--- a/lib/scripts/diffPackageCommits.py
+++ b/lib/scripts/diffPackageCommits.py
@@ -5,7 +5,7 @@
 import subprocess
 import sys
 
-import benchpark.paths
+from benchpark.paths import paths
 
 EXIT_CODE = 0
 
@@ -39,7 +39,7 @@
 def main():
     global EXIT_CODE
     spack_dir = "spack/var/spack/repos/builtin/packages/"
-    benchpark_dir = str(benchpark.paths.benchpark_root) + "/repo/"
+    benchpark_dir = str(paths.benchpark_root) + "/repo/"
 
     # Get the list of packages to process
     if args.packages:
diff --git a/lib/scripts/diffSystemSpecs.py b/lib/scripts/diffSystemSpecs.py
index 9bc279f40..fa6c8c029 100644
--- a/lib/scripts/diffSystemSpecs.py
+++ b/lib/scripts/diffSystemSpecs.py
@@ -7,9 +7,9 @@
 import yaml
 from deepdiff import DeepDiff
 
-import benchpark.paths
+from benchpark.paths import paths
 
-sys.path.append(str(benchpark.paths.benchpark_home) + "/spack/lib/spack")
+sys.path.append(str(paths.benchpark_home) + "/spack/lib/spack")
 import llnl.util.tty.color as color  # noqa: E402