diff --git a/REFACTOR.md b/REFACTOR.md
new file mode 100644
index 0000000..638c972
--- /dev/null
+++ b/REFACTOR.md
@@ -0,0 +1,52 @@
+- Require all app names be set somewhere in the app registry, even if no variables need to
+  be supplied (such as "gnome," which just calls a script based on scheme). This helps
+  explicitly define the scope of "*" for applications, and can allow users to keep their
+  config files without involving them in any `autoconf` call.
+- `scheme: auto` is a valid specification, but it will always resolve to either `light` or
+  `dark`. "auto" is not a valid scheme choice when it comes to naming, but it can be used
+  when making `autoconf` calls to set palettes that reflect the scheme that is currently
+  set (just think of the analogous setting in the browser: auto just means to infer and
+  set the local scheme to whatever the system scheme is set to).
+- Due `/call`, we no longer have explicit, hard-coded scheme commends in `set_theme.py`.
+  Calls to GNOME's portal or to MacOS system settings can now just be seen as another
+  "app" with a configurable script, reactive to the passed scheme option.
+- Here's the palette/scheme spec model
+  * If specific `scheme` and `palette` are provided, files prefixed with
+    `<scheme>-<palette>`, `any-<palette>`, or `<scheme>-any` are matched, in that order,
+    for each unique file tail, for each app.
+  * If `palette` is provided by `scheme` is not, it defaults to `auto` and will attempt to
+    infer a specific value, yielding the same case as above.
+  * If `scheme` cannot be inferred when `auto`, or is explicitly set to `any`, only
+    `any-<palette>` file prefixes are matched. The idea here is that `any` indicates that
+    a theme file is explicitly indifferent to the specification of that option, and won't
+    interfere in an unintended way. The term `none` would work exactly the same here;
+    `any` seems like it might be misleading, indicating it will match with any specific
+    palette. In any case (no pun intended), palettes should create files with an `any`
+    scheme if want to be considered as a possible setting when the `scheme` is any option,
+    i.e., `light/dark/any`.
+  * The same goes for `palette`, although it will default to `any` when unspecified. Thus,
+    only commands/files that change `scheme` will be considered when `palette` isn't
+    given. (I suppose we could also consider an `auto` default here that attempts to
+    determine app-specific palettes that are currently set, and switch to their opposite
+    `scheme` counterparts if available. You could still explicitly provide `any` to ensure
+    you just isolate the `scheme` switch, but `auto` could allow something like a dark to
+    light switch that applies to gnome (only supports scheme), changes kitty to
+    "tone4-light" (a light counterpart the currently set palette is available), and
+    Discord remains the same (as a hypothetical app for which we've created a dark palette
+    but no a light one)). I guess the main takeaway with `any`/`auto` is the following: if
+    `auto` can resolve to the concrete option currently set for a given app, behave as if
+    that option was given. When `any` is provided (or `auto` fails to infer a concrete
+    setting), _isolate_ that property (either `scheme` or `palette`) and ensure it doesn't
+    change (even when another might, and doing so by only matching theme files that have
+    actually used `any`, indicating they actually deliver on the agreed upon behavior
+    here).
+  * If neither are given, (depending on what we decide), both would be `auto` and should
+    do nothing (simply determine the `scheme` and `palette` currently set, requiring no
+    updates). If both are `any`, this should also do nothing; `any` is meant to "freeze"
+    that property, so we'd just be freezing both of the possible variables. One or both of
+    these options could serve as a meaningful refresh, however, either re-symlinking the
+    relevant/expected files and/or calling the refresh commands for each apps to ensure
+    expected settings are freshly applied.
+- Config TOML accepts either `config_dir` or `config_map`, nothing else and only one of
+  the two.
+- Refresh scripts should likely specify a shell shabang at the top of the file
diff --git a/autoconf/__init__.py b/autoconf/__init__.py
index e69de29..4c18f26 100644
--- a/autoconf/__init__.py
+++ b/autoconf/__init__.py
@@ -0,0 +1 @@
+from autoconf.config import ConfigManager
diff --git a/autoconf/__main__.py b/autoconf/__main__.py
index 4fc1567..316b369 100644
--- a/autoconf/__main__.py
+++ b/autoconf/__main__.py
@@ -1,22 +1,101 @@
 import argparse
 
-from gen_theme import add_gen_subparser
-from set_theme import add_set_subparser
+import util
+#from gen_theme import generate_theme_files
+from autoconf.config import ConfigManager
 
 
+def add_set_subparser(subparsers):
+    def update_app_settings(args):
+        cm = ConfigManager(args.config_dif)
+        cm.update_apps(
+            apps=args.apps,
+            scheme=args.scheme,
+            palette=args.palette,
+        )
+
+    parser = subparsers.add_parser(
+        'set',
+        description='Generate theme files for various applications. Uses a template (in TOML ' \
+                  + 'format) to map application-specific config keywords to colors (in JSON '  \
+                  + 'format).' 
+    )
+    parser.add_argument(
+        '-p', '--palette',
+        required = False,
+        default  = "any",
+        help     = 'Palette name, must match a folder in themes/'
+    )
+    parser.add_argument(
+        '-s', '--scheme',
+        required = False,
+        default  = "any",
+        help     = 'Preferred lightness scheme, either "light" or "dark".'
+    )
+    parser.add_argument(
+        '-a', '--apps',
+        required = False,
+        default  = "any",
+        type     = lambda s: s.split(',') if s != '*' else s
+        help     = 'Application target for theme. App must be present in the registry. ' \
+                 + 'Use "*" to apply to all registered apps'
+    )
+    parser.set_defaults(func=update_app_settings)
+
+def add_gen_subparser(subparsers):
+    parser = subparsers.add_parser(
+        'gen',
+        description='Generate theme files for various applications. Uses a template (in TOML ' \
+                  + 'format) to map application-specific config keywords to colors (in JSON '  \
+                  + 'format).' 
+    )
+    parser.add_argument(
+        '-a', '--app',
+        required=True,
+        help='Application target for theme. Supported: ["kitty"]'
+    )
+    parser.add_argument(
+        '-p', '--palette',
+        required=True,
+        help='Palette to use for template mappings. Uses local "theme/<palette>/colors.json".'
+    )
+    parser.add_argument(
+        '-t', '--template',
+        default=None,
+        help='Path to TOML template file. If omitted, app\'s default template path is used.' \
+           + 'If a directory is provided, all TOML files in the folder will be used.'
+    )
+    parser.add_argument(
+        '-o', '--output',
+        default=None,
+        help='Output file path for theme. If omitted, app\'s default theme output path is used.'
+    )
+    parser.set_defaults(func=generate_theme_files)
+
+
+# central argparse entry point
 parser = argparse.ArgumentParser(
     'autoconf',
     description='Generate theme files for various applications. Uses a template (in TOML ' \
               + 'format) to map application-specific config keywords to colors (in JSON '  \
               + 'format).' 
 )
+parser.add_argument(
+    '-c', '--config-dir',
+    default = util.xdg_config_path(),
+    type    = util.absolute_path,
+    help    = 'Path to config directory'
+)
+
+# add subparsers
 subparsers = parser.get_subparsers()
-add_gen_subparser(subparsers)
+#add_gen_subparser(subparsers)
 add_set_subparser(subparsers)
 
-args = parser.parse_args()
 
 if __name__ == '__main__':
+    args = parser.parse_args()
+
     if 'func' in args:
         args.func(args)
     else:
diff --git a/autoconf/config.py b/autoconf/config.py
new file mode 100644
index 0000000..e654a20
--- /dev/null
+++ b/autoconf/config.py
@@ -0,0 +1,370 @@
+import os
+import json
+import inspect
+import tomllib
+import argparse
+import subprocess
+from pathlib import Path
+
+from colorama import Fore, Back, Style
+
+from autoconf import util
+
+
+class ConfigManager:
+    def __init__(
+        self,
+        config_dir=None,
+        disable_registry=False,
+    ):
+        '''
+        Configuration manager class
+
+        Parameters:
+            config_dir: config parent directory housing expected files (registry,
+                        app-specific conf files, etc). Defaults to
+                        ``"$XDG_CONFIG_HOME/autoconf/"``.
+            disable_registry: disable checks for a registry file in the ``config_dir``.
+                              Should really only be set when using this programmatically
+                              and manually supplying app settings.
+        '''
+        if config_dir == None:
+            config_dir = util.xdg_config_path()
+
+        self.config_dir = util.absolute_path(config_dir)
+        self.apps_dir   = Path(self.config_dir, 'apps')
+
+        self.app_registry = {}
+
+        self._check_paths()
+
+        if not disable_registry:
+            self._check_registry()
+
+    def _check_paths(self):
+        '''
+        Check necessary paths for existence.
+
+        Regardless of programmatic use or ``disable_registry``, we need to a valid
+        ``config_dir`` and it must have an ``apps/`` subdirectory (otherwise there are
+        simply no files to act on, not even when manually providing app settings).
+        '''
+        # throw error if config dir doesn't exist
+        if not self.config_dir.exists():
+            raise ValueError(
+                f'Config directory "{self.config_dir}" doesn\'t exist.'
+            )
+        
+        # throw error if apps dir doesn't exist or is empty
+        if not self.apps_dir.exists() or not list(self.apps_dir.iterdir()):
+            raise ValueError(
+                f'Config directory "{self.config_dir}" must have an "apps/" subdirectory.'
+            )
+
+    def _check_registry(self):
+        registry_path = Path(self.config_dir, 'app_registry.toml')
+
+        self.app_registry = {}
+        if not registry_path.exists():
+            print(
+                Fore.YELLOW \
+                + f'No registry file found at expected location "{registry_path}"'
+            )
+            return
+
+        app_registry = tomllib.load(registry_path.open('rb'))
+
+        if 'app' not in app_registry:
+            print(
+                Fore.YELLOW \
+                + f'Registry file found but is either empty or incorrectly formatted (no "app" key).'
+            )
+
+        self.app_registry = app_registry.get('app', {})
+
+    def resolve_scheme(self, scheme):
+        # if scheme == 'auto':
+        #     os_cmd_groups = {
+        #         'Linux': (
+        #             "gsettings get org.gnome.desktop.interface color-scheme",
+        #             lambda r: r.split('-')[1][:-1],
+        #         ),
+        #         'Darwin': (),
+        #     }
+
+        #     osname = os.uname().sysname
+        #     os_group = os_cmd_groups.get(osname, [])
+
+        #     for cmd in cmd_list:
+        #         subprocess.check_call(cmd.format(scheme=scheme).split())
+
+        # return scheme
+
+        if scheme == 'auto':
+            return 'any'
+
+        return scheme
+
+    def resolve_palette(self, palette):
+        if palette == 'auto':
+            return 'any'
+
+        return palette
+
+    def app_config_map(self, app_name):
+        '''
+        Get the config map for a provided app.
+
+        The config map is a dict mapping from config file **path names** to their absolute
+        path locations. That is, 
+
+        ```sh
+        <config_path_name> -> <config_dir>/apps/<app_name>/<subdir>/<palette>-<scheme>.<config_path_name>
+        ```
+
+        For example,
+
+        ```
+        palette1-light.conf.ini -> ~/.config/autoconf/apps/user/palette1-light.conf.ini
+        palette2-dark.app.conf -> ~/.config/autoconf/apps/generated/palette2-dark.app.conf
+        ```
+
+        This ensures we have unique config names pointing to appropriate locations (which
+        is mostly important when the same config file names are present across ``user``
+        and ``generated`` subdirectories).
+        '''
+        # first look in "generated", then overwrite with "user"
+        file_map = {}
+        app_dir  = Path(self.apps_dir, app_name)
+        for subdir in ['generated', 'user']:
+            subdir_path = Path(app_dir, subdir)
+
+            if not subdir_path.is_dir():
+                continue
+
+            for conf_file in subdir_path.iterdir():
+                file_map[conf_file.name] = conf_file
+
+        return file_map
+
+    def get_matching_configs(
+        self, 
+        app_name,
+        scheme='auto',
+        palette='auto',
+    ) -> dict[str, str]:
+        '''
+        Get app config files that match the provided scheme and palette.
+
+        Unique config file path names are written to the file map in order of specificity.
+        All config files follow the naming scheme ``<palette>-<scheme>.<path-name>``,
+        where ``<palette>-<scheme>`` is the "theme part" and ``<path-name>`` is the "conf
+        part." For those config files with the same "conf part," only the entry with the
+        most specific "theme part" will be stored. By "most specific," we mean those
+        entries with the fewest possible components named ``any``, with ties broken in
+        favor of a more specific ``palette`` (the only "tie" really possible here is when
+        `any-<scheme>` and `<palette>-any` are both available, in which case the latter
+        will overwrite the former).
+        '''
+        app_dir = Path(self.apps_dir, app_name)
+
+        scheme  = self.resolve_scheme(scheme)
+        palette = self.resolve_palette(palette)
+
+        # now match theme files in order of inc. specificity; for each unique config file
+        # tail, only the most specific matching file sticks
+        file_parts = []
+        app_config_map = self.app_config_map(app_name)
+        for pathname in app_config_map:
+            parts = pathname.split('.')
+
+            if len(parts) < 2:
+                print(f'Filename "{filename}" incorrectly formatted, ignoring')
+                continue
+
+            theme_part, conf_part = parts[0], '.'.join(parts[1:])
+            file_parts.append((theme_part, conf_part, pathname))
+
+        theme_prefixes = [
+            'any-any',
+            f'any-{scheme}',
+            f'{palette}-any',
+            f'{palette}-{scheme}'
+        ]
+
+        matching_file_map = {}
+        for theme_prefix in theme_prefixes:
+            for theme_part, conf_part, pathname in file_parts:
+                if theme_part == theme_prefix:
+                    matching_file_map[conf_part] = app_config_map[pathname]
+
+        return matching_file_map
+
+    def get_matching_scripts(
+        self,
+        app_name,
+        scheme='any',
+        palette='any',
+    ):
+        '''
+        Execute matching scripts in the app's ``call/`` directory.
+
+        Scripts need to be placed in 
+
+        ```sh
+        <config_dir>/apps/<app_name>/call/<palette>-<scheme>.sh
+        ```
+
+        and are matched using the same heuristic employed by config file symlinking
+        procedure (see ``get_matching_configs()``).
+        '''
+        app_dir  = Path(self.apps_dir, app_name)
+        call_dir = Path(app_dir, 'call')
+        
+        if not call_dir.is_dir():
+            return
+
+        theme_prefixes = [
+            'any-any',
+            f'any-{scheme}',
+            f'{palette}-any',
+            f'{palette}-{scheme}'
+        ]
+
+        # do it this way to keep order for downstream exec
+        script_list = []
+        for theme_prefix in theme_prefixes:
+            for script_path in call_dir.iterdir():
+                theme_part = script_path.stem
+                if theme_part == theme_prefix:
+                    script_list.append(script_path)
+
+        return list(set(script_list))
+
+    def update_app_config(
+        self,
+        app_name,
+        app_settings = None,
+        scheme       = 'any',
+        palette      = 'any',
+    ):
+        '''
+        Perform full app config update process, applying symlinks and running scripts.
+
+        Note that this explicitly accepts app settings to override or act in place of
+        missing app details in the app registry file. This is mostly to provide more
+        programmatic control and test settings without needing them present in the
+        registry file. The ``update_apps()`` method, however, **will** more strictly
+        filter out those apps not in the registry, accepting a list of app keys that
+        ultimately call this method.
+
+        Note: symlinks point **from** the target location **to** the known internal config
+        file; can be a little confusing.
+        '''
+        if app_settings is None:
+            app_settings = self.app_registry.get(app_name, {})
+
+        if 'config_dir' in app_settings and 'config_map' in app_settings:
+            print(f'App "{app_name}" incorrectly configured, skipping')
+            return
+
+        to_symlink: list[tuple[Path, Path]] = []
+        file_map = self.get_matching_configs(
+            app_name,
+            scheme=scheme,
+            palette=palette,
+        )
+        if 'config_dir' in app_settings:
+            for config_tail, full_path in file_map.items():
+                to_symlink.append((
+                    util.absolute_path(Path(app_settings['config_dir'], config_tail)), # point from real config dir
+                    full_path, # to internal config location
+                ))
+        elif 'config_map' in app_settings:
+            for config_tail, full_path in file_map.items():
+                # app's config map points config tails to absolute paths
+                if config_tail in app_settings['config_map']:
+                    to_symlink.append((
+                        abs_pat(Path(app_settings['config_map'][config_tail])), # point from real config path
+                        full_path, # to internal config location
+                    ))
+
+        links_succ = []
+        links_fail = []
+        for from_path, to_path in to_symlink:
+            if not to_path.exists():
+                print(f'Internal config path "{to_path}" doesn\'t exist, skipping')
+                links_fail.append((from_path, to_path))
+                continue
+
+            if not from_path.parent.exists():
+                print(f'Target config parent directory for "{from_path}" doesn\'t exist, skipping')
+                links_fail.append((from_path, to_path))
+                continue
+
+            # if config file being symlinked exists & isn't already a symlink (i.e.,
+            # previously set by this script), throw an error. 
+            if from_path.exists() and not from_path.is_symlink():
+                print(
+                    f'Symlink target "{from_path}" exists and isn\'t a symlink, NOT overwriting;' \
+                   + ' please first manually remove this file so a symlink can be set.'
+                )
+                links_fail.append((from_path, to_path))
+                continue
+            else:
+                # if path doesn't exist, or exists and is symlink, remove the symlink in
+                # preparation for the new symlink setting
+                from_path.unlink(missing_ok=True)
+
+            #print(f'Linking [{from_path}] -> [{to_path}]')
+            from_path.symlink_to(to_path)
+            links_succ.append((from_path, to_path))
+
+            # run matching scripts for app-specific reload
+            # TODO: store the status of this cmd & print with the messages
+            script_list = self.get_matching_scripts(
+                app_name,
+                scheme=scheme,
+                palette=palette,
+            )
+            for script in script_list:
+                print(Fore.BLUE + f'> Running script "{script.relative_to(self.config_dir}"')
+                output = subprocess.check_output(str(script), shell=True)
+                print(
+                    Fore.BLUE + Style.DIM + f'-> Captured script output "{output.decode().strip()}"' + Style.RESET
+                )
+
+        for from_p, to_p in links_succ:
+            from_p = from_p
+            to_p   = to_p.relative_to(self.config_dir)
+            print(Fore.GREEN + f'> {app_name} :: {from_p} -> {to_p}')
+
+        for from_p, to_p in links_fail:
+            from_p = from_p
+            to_p   = to_p.relative_to(self.config_dir)
+            print(Fore.RED + f'> {app_name} :: {from_p} -> {to_p}')
+
+    def update_apps(
+        self,
+        apps: str | list[str] = '*',
+        scheme                = 'any',
+        palette               = 'any',
+    ):
+        if apps == '*':
+            # get all registered apps
+            app_list = list(self.app_registry.keys())
+        else:
+            # get requested apps that overlap with registry
+            app_list = [a for a in app_list if a in app_registry]
+
+        if not app_list:
+            print(f'None of the apps "apps" are registered, exiting')
+            return
+
+        for app_name in app_list:
+            self.update_app_config(
+                app_name,
+                app_settings=app_registry[app_name],
+                scheme=scheme,
+                palette=palette,
+            )
diff --git a/autoconf/set_theme.py b/autoconf/set_theme.py
deleted file mode 100644
index c077924..0000000
--- a/autoconf/set_theme.py
+++ /dev/null
@@ -1,146 +0,0 @@
-import argparse
-import inspect
-import subprocess
-import json
-import os
-import tomllib as toml
-from pathlib import Path
-
-from colorama import Fore
-
-def add_set_subparser(subparsers):
-    parser = subparsers.add_parser(
-        'set',
-        description='Generate theme files for various applications. Uses a template (in TOML ' \
-                  + 'format) to map application-specific config keywords to colors (in JSON '  \
-                  + 'format).' 
-    )
-    parser.add_argument(
-        '-p', '--palette',
-        required=True,
-        help='Palette name, must match a folder in themes/'
-    )
-    parser.add_argument(
-        '-s', '--scheme',
-        required=True,
-        help='Preferred lightness scheme, either "light" or "dark".'
-    )
-    parser.add_argument(
-        '-a', '--app',
-        required=True,
-        help='Application target for theme. App must be present in the registry. ' \
-           + 'Use "*" to apply to all registered apps'
-    )
-    parser.set_defaults(func=update_theme_settings)
-
-
-def get_running_path():
-    calling_module = inspect.getmodule(inspect.stack()[-1][0])
-    return Path(calling_module.__file__).parent
-
-def os_scheme_settings(scheme):
-    '''
-    Groups of settings/commands to invoke globally based on the provided `scheme`. This
-    may control things like default app light/dark behavior, for instance.
-    '''
-    os_cmd_groups = {
-        'Linux': [
-            "gsettings set org.gnome.desktop.interface color-scheme 'prefer-{scheme}'",
-        ],
-        'Darwin': [],
-    }
-
-    if scheme not in ['light', 'dark']: return
-    osname = os.uname().sysname
-    cmd_list = os_cmd_groups.get(osname, [])
-
-    for cmd in cmd_list:
-        subprocess.check_call(cmd.format(scheme=scheme).split())
-
-def update_theme_settings():
-    osname       = os.uname().sysname
-    basepath     = get_running_path()
-    app_registry = toml.load(Path(basepath, 'app_registry.toml').open('rb'))
-    app_registry = app_registry.get('app', {})
-
-    if args.app not in app_registry and args.app != '*':
-        print(f'App {args.app} not registered, exiting')
-        return
-
-    app_list = []
-    if args.app == '*':
-        app_list = list(app_registry.items())
-    else:
-        app_list = [(args.app, app_registry[args.app])]
-
-    links_succ = {}
-    links_fail = {}
-    for app_name, app_settings in app_list:
-        config_dir  = Path(app_settings['config_dir']).expanduser()
-        config_file = app_settings['config_file']
-        config_path = Path(config_dir, config_file)
-
-        if osname not in app_settings['supported_oses']:
-            print(f'OS [{osname}] not support for app [{app_name}]')
-            continue
-
-        if app_settings['external_theme']:
-            # symlink from "current-theme.conf" in app's config-dir ...
-            from_conf_path = Path(config_dir, 'current-theme.conf')
-
-            # ... to appropriate generated theme path here in autoconf
-            to_conf_path = Path(
-                basepath,
-                f'themes/{args.palette}/apps/{app_name}/generated/{args.scheme}.conf'
-            )
-        else:
-            # symlink from the canonical config file ...
-            from_conf_path = config_path
-
-            # ... to appropriate theme variant
-            to_conf_path = Path(
-                config_dir, 
-                f'{app_name}-{args.palette}-{args.scheme}{config_path.suffix}'
-            )
-
-        if not to_conf_path.exists():
-            print(
-                f'Expected symlink target [{to_conf_path}] doesn\'t exist, skipping'
-            )
-            links_fail[app_name] = (from_conf_path.name, to_conf_path.name)
-            continue
-
-        # if config file being symlinked exists & isn't already a symlink (i.e.,
-        # previously set by this script), throw an error. 
-        if from_conf_path.exists() and not from_conf_path.is_symlink():
-            print(
-                f'Symlink origin [{from_conf_path}] exists and isn\'t a symlink; please ' \
-               + 'first manually remove this file so this script can set the symlink.'
-            )
-            links_fail[app_name] = (from_conf_path.name, to_conf_path.name)
-            continue
-        else:
-            # if path doesn't exist, or exists and is symlink, remove the symlink in
-            # preparation for the new symlink setting
-            from_conf_path.unlink(missing_ok=True)
-
-        print(f'Linking [{from_conf_path}] -> [{to_conf_path}]')
-
-        # run color scheme live-reload for app, if available
-        # TODO: store the status of this cmd & print with the messages
-        if 'refresh_cmd' in app_settings:
-            subprocess.check_call(app_settings['refresh_cmd'], shell=True)
-
-        from_conf_path.symlink_to(to_conf_path)
-        links_succ[app_name] = (from_conf_path.name, to_conf_path.name)
-
-    for app, (from_p, to_p) in links_succ.items():
-        print(Fore.GREEN + f'> {app} :: {from_p} -> {to_p}')
-
-    for app, (from_p, to_p) in links_fail.items():
-        print(Fore.RED + f'> {app} :: {from_p} -> {to_p}')
-
-
-if __name__ == '__main__':
-    os_scheme_settings(args.scheme)
-    update_theme_settings()
diff --git a/autoconf/gen_theme.py b/autoconf/theme.py
similarity index 65%
rename from autoconf/gen_theme.py
rename to autoconf/theme.py
index 12bd8fc..1e5a60a 100644
--- a/autoconf/gen_theme.py
+++ b/autoconf/theme.py
@@ -4,41 +4,6 @@ import json
 import tomllib as toml
 from pathlib import Path
 
-def get_running_path():
-    calling_module = inspect.getmodule(inspect.stack()[-1][0])
-    return Path(calling_module.__file__).parent
-
-
-def add_gen_subparser(subparsers):
-    parser = subparsers.add_parser(
-        'gen',
-        description='Generate theme files for various applications. Uses a template (in TOML ' \
-                  + 'format) to map application-specific config keywords to colors (in JSON '  \
-                  + 'format).' 
-    )
-    parser.add_argument(
-        '-a', '--app',
-        required=True,
-        help='Application target for theme. Supported: ["kitty"]'
-    )
-    parser.add_argument(
-        '-p', '--palette',
-        required=True,
-        help='Palette to use for template mappings. Uses local "theme/<palette>/colors.json".'
-    )
-    parser.add_argument(
-        '-t', '--template',
-        default=None,
-        help='Path to TOML template file. If omitted, app\'s default template path is used.' \
-           + 'If a directory is provided, all TOML files in the folder will be used.'
-    )
-    parser.add_argument(
-        '-o', '--output',
-        default=None,
-        help='Output file path for theme. If omitted, app\'s default theme output path is used.'
-    )
-    parser.set_defaults(func=generate_theme_files)
-
 
 # separation sequences to use base on app
 app_sep_map = {
diff --git a/autoconf/themes/tone4/apps/kitty/generated/dark.conf b/autoconf/themes/tone4/apps/kitty/generated/dark.conf
deleted file mode 100644
index 2f3772f..0000000
--- a/autoconf/themes/tone4/apps/kitty/generated/dark.conf
+++ /dev/null
@@ -1,21 +0,0 @@
-background #1b1b1b
-foreground #c6c6c6
-selection_background #303030
-selection_foreground #ababab
-cursor #d4d4d4
-color0 #262626
-color8 #262626
-color1 #ed625d
-color9 #ed625d
-color2 #34a543
-color10 #34a543
-color3 #a68f03
-color11 #a68f03
-color4 #618eff
-color12 #618eff
-color5 #ed625d
-color13 #ed625d
-color6 #618eff
-color14 #618eff
-color7 #d4d4d4
-color15 #d4d4d4
\ No newline at end of file
diff --git a/autoconf/themes/tone4/apps/kitty/generated/light.conf b/autoconf/themes/tone4/apps/kitty/generated/light.conf
deleted file mode 100644
index 972d9b9..0000000
--- a/autoconf/themes/tone4/apps/kitty/generated/light.conf
+++ /dev/null
@@ -1,21 +0,0 @@
-background #f1f1f1
-foreground #262626
-selection_background #ababab
-selection_foreground #303030
-cursor #262626
-color0 #1b1b1b
-color8 #1b1b1b
-color1 #c25244
-color9 #c25244
-color2 #298835
-color10 #298835
-color3 #897600
-color11 #897600
-color4 #4e75d4
-color12 #4e75d4
-color5 #c25244
-color13 #c25244
-color6 #4e75d4
-color14 #4e75d4
-color7 #d4d4d4
-color15 #d4d4d4
\ No newline at end of file
diff --git a/autoconf/themes/tone4/apps/kitty/templates/dark.toml b/autoconf/themes/tone4/apps/kitty/templates/dark.toml
deleted file mode 100644
index 9b8900d..0000000
--- a/autoconf/themes/tone4/apps/kitty/templates/dark.toml
+++ /dev/null
@@ -1,40 +0,0 @@
-# base settings
-background           = 'black.bg+1'
-foreground           = 'black.fg+3'
-
-selection_background = 'black.bg+3'
-selection_foreground = 'black.m+4'
-
-cursor               = 'black.fg+2'
-
-# black
-color0               = 'black.bg+2'
-color8               = 'black.bg+2'
-
-# red
-color1               = 'red.m+2'
-color9               = 'red.m+2'
-
-# green
-color2               = 'green.m+2'
-color10              = 'green.m+2'
-
-# yellow
-color3               = 'yellow.m+2'
-color11              = 'yellow.m+2'
-
-# blue
-color4               = 'blue.m+2'
-color12              = 'blue.m+2'
-
-# purple (red)
-color5               = 'red.m+2'
-color13              = 'red.m+2'
-
-# cyan (blue)
-color6               = 'blue.m+2'
-color14              = 'blue.m+2'
-
-## white
-color7               = 'black.fg+2'
-color15              = 'black.fg+2'
diff --git a/autoconf/themes/tone4/apps/kitty/templates/light.toml b/autoconf/themes/tone4/apps/kitty/templates/light.toml
deleted file mode 100644
index 9e862d9..0000000
--- a/autoconf/themes/tone4/apps/kitty/templates/light.toml
+++ /dev/null
@@ -1,40 +0,0 @@
-# base settings
-background           = 'black.fg+1'
-foreground           = 'black.bg+2'
-
-selection_background = 'black.m+4'
-selection_foreground = 'black.bg+3'
-
-cursor               = 'black.bg+2'
-
-# black
-color0               = 'black.bg+1'
-color8               = 'black.bg+1'
-
-# red
-color1               = 'red.m+0'
-color9               = 'red.m+0'
-
-# green
-color2               = 'green.m+0'
-color10              = 'green.m+0'
-
-# yellow
-color3               = 'yellow.m+0'
-color11              = 'yellow.m+0'
-
-# blue
-color4               = 'blue.m+0'
-color12              = 'blue.m+0'
-
-# purple (red)
-color5               = 'red.m+0'
-color13              = 'red.m+0'
-
-# cyan (blue)
-color6               = 'blue.m+0'
-color14              = 'blue.m+0'
-
-## white
-color7               = 'black.fg+2'
-color15              = 'black.fg+2'
diff --git a/autoconf/themes/tone4/colors.json b/autoconf/themes/tone4/colors.json
deleted file mode 100644
index 27cb9b3..0000000
--- a/autoconf/themes/tone4/colors.json
+++ /dev/null
@@ -1,107 +0,0 @@
-{
-  "red": {
-    "bg+0": "#1c0d0a",
-    "bg+1": "#2d1412",
-    "bg+2": "#401a17",
-    "bg+3": "#531f1d",
-    "bg+4": "#652624",
-    "m-4": "#782d2b",
-    "m-3": "#8b3633",
-    "m-2": "#9d3e3b",
-    "m-1": "#b14643",
-    "m+0": "#c25244",
-    "m+1": "#d95854",
-    "m+2": "#ed625d",
-    "m+3": "#f27870",
-    "m+4": "#f68c83",
-    "fg+4": "#faa097",
-    "fg+3": "#fdb3ab",
-    "fg+2": "#fec6c0",
-    "fg+1": "#ffdad3",
-    "fg+0": "#ffede9"
-  },
-  "yellow": {
-    "bg+0": "#151100",
-    "bg+1": "#211b00",
-    "bg+2": "#2d2500",
-    "bg+3": "#393000",
-    "bg+4": "#453b00",
-    "m-4": "#524600",
-    "m-3": "#5f5100",
-    "m-2": "#6d5d00",
-    "m-1": "#7a6900",
-    "m+0": "#897600",
-    "m+1": "#978200",
-    "m+2": "#a68f03",
-    "m+3": "#b29c34",
-    "m+4": "#bfaa53",
-    "fg+4": "#cbb770",
-    "fg+3": "#d6c58c",
-    "fg+2": "#e1d3a9",
-    "fg+1": "#ebe2c5",
-    "fg+0": "#f5f0e2"
-  },
-  "green": {
-    "bg+0": "#081406",
-    "bg+1": "#0e1f0c",
-    "bg+2": "#0f2c10",
-    "bg+3": "#103814",
-    "bg+4": "#114518",
-    "m-4": "#15521d",
-    "m-3": "#1a5f23",
-    "m-2": "#1e6c29",
-    "m-1": "#247a2f",
-    "m+0": "#298835",
-    "m+1": "#2e973b",
-    "m+2": "#34a543",
-    "m+3": "#56b15a",
-    "m+4": "#71bc72",
-    "fg+4": "#8ac789",
-    "fg+3": "#a2d3a0",
-    "fg+2": "#badeb8",
-    "fg+1": "#d1e9cf",
-    "fg+0": "#e8f4e7"
-  },
-  "blue": {
-    "bg+0": "#0f101b",
-    "bg+1": "#151b2f",
-    "bg+2": "#1a2544",
-    "bg+3": "#202f59",
-    "bg+4": "#263a6e",
-    "m-4": "#2d4582",
-    "m-3": "#355196",
-    "m-2": "#3d5daa",
-    "m-1": "#4669bf",
-    "m+0": "#4e75d4",
-    "m+1": "#5781ea",
-    "m+2": "#618eff",
-    "m+3": "#7b9bff",
-    "m+4": "#91a9ff",
-    "fg+4": "#a6b7ff",
-    "fg+3": "#b9c5ff",
-    "fg+2": "#cbd3ff",
-    "fg+1": "#dde1ff",
-    "fg+0": "#eef0fe"
-  },
-  "black": {
-    "bg+0": "#111111",
-    "bg+1": "#1b1b1b",
-    "bg+2": "#262626",
-    "bg+3": "#303030",
-    "bg+4": "#3b3b3b",
-    "m-4": "#474747",
-    "m-3": "#525252",
-    "m-2": "#5e5e5e",
-    "m-1": "#6a6a6a",
-    "m+0": "#777777",
-    "m+1": "#848484",
-    "m+2": "#919191",
-    "m+3": "#9e9e9e",
-    "m+4": "#ababab",
-    "fg+4": "#b9b9b9",
-    "fg+3": "#c6c6c6",
-    "fg+2": "#d4d4d4",
-    "fg+1": "#e2e2e2",
-    "fg+0": "#f1f1f1"
-  }
-}
diff --git a/autoconf/util.py b/autoconf/util.py
new file mode 100644
index 0000000..00b78a8
--- /dev/null
+++ b/autoconf/util.py
@@ -0,0 +1,9 @@
+from pathlib import Path
+from xdg import BaseDirectory
+
+
+def absolute_path(path: str | Path) -> Path:
+    return Path(path).expanduser().absolute()
+    
+def xdg_config_path():
+    return Path(BaseDirectory.save_config_path('autoconf'))
diff --git a/config/app_registry.toml b/config/app_registry.toml
deleted file mode 100644
index 00c39fd..0000000
--- a/config/app_registry.toml
+++ /dev/null
@@ -1,42 +0,0 @@
-# App registry -- apps eligible for theme switching
-#
-# Each app must be register under the "app" directive, i.e., as "[app.<app-name>]"
-#
-# Option details:
-# - external_theme: if False (default), indicates an app of type 1 as per the README. That
-#   is, an external theme file cannot be used, and theme switching will involve switch the
-#   canonical config setting. If True, the app's theme can be set through an external theme
-#   file.
-# - support_os: OSes that support theme switching according to the implemented paths.
-#   Accepts a list of `uname -s` strings to match system.
-# - refresh_cmd: a command to run for live refreshing the application's color scheme after
-#   it's been set for running instances.
-#
-# Default example 
-# [app.default]
-# external_theme = False
-# config_dir     = '~/.config/default/'
-# config_file    = 'default.conf'
-# refresh_cmd    = 'app reload-config'
-# 
-
-[app.kitty]
-external_theme = true
-config_dir     = '~/.config/kitty/'
-config_file    = 'kitty.conf'
-supported_oses = ['Linux', 'Darwin']
-refresh_cmd    = 'kill -s USR1 $(pgrep kitty)'
-
-[app.sway]
-external_theme = false
-config_dir     = '~/.config/sway/'
-config_file    = 'config'
-supported_oses = ['Linux']
-#refresh_cmd    = 'swaymsg reload'
-
-[app.waybar]
-external_theme = false
-config_dir     = '~/.config/waybar/'
-config_file    = 'style.css'
-supported_oses = ['Linux']
-refresh_cmd    = 'swaymsg reload'
diff --git a/docs/_templates/autosummary.md b/docs/_templates/autosummary.md
new file mode 100644
index 0000000..216f1df
--- /dev/null
+++ b/docs/_templates/autosummary.md
@@ -0,0 +1,9 @@
+# {{ fullname | escape }}
+
+```{automodule}
+{{ fullname }}
+:members:
+:undoc-members:
+:show-inheritance:
+:imported-members:
+```
diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst
new file mode 100644
index 0000000..6d5a51d
--- /dev/null
+++ b/docs/_templates/autosummary/module.rst
@@ -0,0 +1,8 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :imported-members:
+
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..0b3cf88
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,38 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = '<project-name>'
+copyright = '2024, Sam Griesemer'
+author = 'Sam Griesemer'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "myst_parser",
+]
+autosummary_generate = True
+autosummary_imported_members = True
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'furo'
+html_static_path = ['_static']
+#html_sidebars = {
+#    '**': ['/modules.html'],
+#}
+
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..aa6cc03
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,29 @@
+# `autoconf` package docs 
+{ref}`genindex`
+{ref}`modindex`
+{ref}`search`
+
+```{eval-rst}
+.. autosummary::
+   :nosignatures:
+
+    # list modules here for quick links
+```
+
+```{toctree}
+:maxdepth: 3
+:caption: Autoref
+
+_autoref/autoconf.rst
+```
+
+```{toctree}
+:maxdepth: 3
+:caption: Contents
+
+reference/documentation/index
+reference/site/index
+```
+
+```{include} ../README.md
+```
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000..32bb245
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/reference/documentation/index.md b/docs/reference/documentation/index.md
new file mode 100644
index 0000000..a14cdde
--- /dev/null
+++ b/docs/reference/documentation/index.md
@@ -0,0 +1,8 @@
+# Documentation
+
+```{toctree}
+:hidden:
+
+sphinx
+```
+
diff --git a/docs/reference/documentation/sphinx.md b/docs/reference/documentation/sphinx.md
new file mode 100644
index 0000000..33d6f27
--- /dev/null
+++ b/docs/reference/documentation/sphinx.md
@@ -0,0 +1,111 @@
+# Sphinx
+The primary driver of this package's documentation is Sphinx's `autodoc` extension,
+using the [Furo theme][1]. 
+
+**High-level details**:
+
+- `sphinx-apidoc` generates package-based documentation to the `_autoref/` directory,
+  with navigation available under "Autoref" in the sidebar.
+- Markdown-based documentation files are manually written under the `reference/`
+  directory, showing up under "Contents" in the sidebar.
+
+## Detailed directory structure
+All files are placed under `docs/sphinx`: 
+
+- `_`-prefixed are Sphinx-managed directories
+    * `_build/html/` houses output HTML files
+    * `_autoref/` is the target for module-based RST files written by `autodoc`
+- `reference/`: houses all manually written documentation (totally separate from
+  auto-generated package docs)
+- `conf.py`: single Sphinx configuration file
+- `index.md`: documentation index, setups up a persistent sidebar across all other pages
+
+For manually written documentation under `reference/`, topics are nested as needed. Within
+a nested directory `reference/<topic>`, an `index.md` should created with content like:
+
+```
+# <Topic>
+
+\`\`\`{toctree}
+:hidden:
+
+sub-topic-1.rst
+sub-topic-2.rst
+...
+\`\`\`
+```
+
+This will add the nested directory to the sidebar navigation, using the name set under the
+top-level header. See [Markdown syntax][#markdown-syntax] for more details on the syntax.
+
+## Sphinx autodoc
+Sphinx's `autodoc` extension allows automatic generation of documents according to
+(Python) subpackage structure and available docstrings. A few notes here:
+
+- In the `conf.py` file, autodoc is enabled by adding `"sphinx.ext.autodoc"` to
+  the extensions list. `"sphinx.ext.viewcode"` can also be added to provide
+  links to source code.
+- Documents are actually generated by calling the `sphinx-apidoc` CLI command. The
+  current Makefile uses the following call:
+
+  ```sh
+  sphinx-apidoc --module-first -o docs/sphinx/_autoref/ localsys
+  ```
+
+  This writes the automatically generated docs for modules in the package at the
+  local directory `localsys/` to the `docs/sphinx/_autoref` directory. These are
+  reStructuredText files by default.
+    * `--module-first` places the module-level descriptions at the top of the module page.
+      By default, this is placed at the bottom (oddly), and can be obscured by large lists
+      of subpackages if this flag isn't provided.
+    * See available `sphinx-apidoc` options [here][2], as well as more advanced config
+      [here][3].
+
+
+## Markdown syntax
+The `myst_parser` extension enables Markdown (or something close to it) to be used when
+writing documentation files. The Sphinx directives can be difficult to track, and
+they change slightly under the MyST Markdown syntax. The following are a few common
+blocks:
+
+**Page hierarchies**: the following will generate link hierarchy according to the provided
+pages:
+
+```
+\`\`\`{toctree}
+:maxdepth: <n>
+:caption: <caption>
+:hidden:
+
+example-file-1
+example-file-2
+example-dir/index
+...
+\`\`\`
+```
+
+- `:maxdepth:` limits the depth of nesting
+- `:caption:` title for the group of pages
+- `:hidden:` if provided, links will only show in the sidebar (hidden on the page)
+- Constituent files: listed files will be rendered as a link directly. If a listed file
+  has a `{toctree}` directive, this tree will be rendered in place of the page's link as a
+  dropdown. The dropdown will be named according to the file's top-level heading, and
+  clicking directly on the dropdown header will show that page's content. Files found in
+  the tree will be placed as links under the dropdown, recursively subject to same rules
+  described here.
+
+**Include files**: the following will include file content
+pages:
+
+```
+\`\`\`{include} README.md
+\`\`\`
+```
+
+**Reference directives**
+
+
+[1]: https://pradyunsg.me/furo/
+[2]: https://www.sphinx-doc.org/en/master/man/sphinx-apidoc.html
+[3]: https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#
+
diff --git a/tests/test-config-dir/app_registry.toml b/tests/test-config-dir/app_registry.toml
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test-config-dir/apps/gnome/call/any-dark.sh b/tests/test-config-dir/apps/gnome/call/any-dark.sh
new file mode 100644
index 0000000..7f9dc22
--- /dev/null
+++ b/tests/test-config-dir/apps/gnome/call/any-dark.sh
@@ -0,0 +1 @@
+gsettings set org.gnome.desktop.interface color-scheme 'prefer-dark'
diff --git a/tests/test-config-dir/apps/gnome/call/any-light.sh b/tests/test-config-dir/apps/gnome/call/any-light.sh
new file mode 100644
index 0000000..fcabb84
--- /dev/null
+++ b/tests/test-config-dir/apps/gnome/call/any-light.sh
@@ -0,0 +1 @@
+gsettings set org.gnome.desktop.interface color-scheme 'prefer-light'
diff --git a/tests/test-config-dir/apps/kitty/call/any-any.sh b/tests/test-config-dir/apps/kitty/call/any-any.sh
new file mode 100755
index 0000000..fd9c92e
--- /dev/null
+++ b/tests/test-config-dir/apps/kitty/call/any-any.sh
@@ -0,0 +1 @@
+echo "> Testing script"
diff --git a/tests/test-config-dir/apps/kitty/user/any-any.conf.ini b/tests/test-config-dir/apps/kitty/user/any-any.conf.ini
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test-config-dir/apps/kitty/user/any-light.conf.ini b/tests/test-config-dir/apps/kitty/user/any-light.conf.ini
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test-config-dir/apps/kitty/user/spec-dark.conf b/tests/test-config-dir/apps/kitty/user/spec-dark.conf
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test-config-dir/apps/kitty/user/test-light.conf.aba b/tests/test-config-dir/apps/kitty/user/test-light.conf.aba
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test-config-dir/conf.ini b/tests/test-config-dir/conf.ini
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_config.py b/tests/test_config.py
new file mode 100644
index 0000000..e69de29