diff --git a/shepherd/agent/core.py b/shepherd/agent/core.py
index 1ab2b1b..2f4cddb 100644
--- a/shepherd/agent/core.py
+++ b/shepherd/agent/core.py
@@ -207,9 +207,16 @@ def compile_config(confman, default_config_path, layers_disabled):
     custom_config_path = core_conf["custom_config_path"]
     confman.save_fallback()
 
+    if not core_conf["plugin_dir"]:
+        log.warn("Custom plugin path is empty, won't load custom plugins")
+
     # ====Custom Local Config Layer====
     # If this fails, maintain default config but continue on to Control layer
-    if "custom" not in layers_disabled:
+    if "custom" in layers_disabled:
+        log.info("Custom config layer disabled")
+    elif not custom_config_path:
+        log.warning("Custom config path is empty, skipping custom config layer")
+    else:
         try:
             load_config_layer_and_plugins(confman, custom_config_path)
             log.info(F"Loaded custom config layer from {custom_config_path}")
@@ -223,9 +230,6 @@ def compile_config(confman, default_config_path, layers_disabled):
             log.warning("Falling back to default config.")
             confman.fallback()
 
-    else:
-        log.info("Custom config layer disabled")
-
     # Freeze Shepherd Control related config.
     core_conf = confman.get_config_bundle("shepherd")
     resolve_core_conf_paths(core_conf)
@@ -271,10 +275,10 @@ def core_confspec():
         ("name", StringSpec(helptext="Identifying name for this device")),
         ("hostname", StringSpec(default="", optional=True, helptext="If set, changes the system"
                                 " hostname")),
-        ("plugin_dir", StringSpec(default="~/shepherd-plugins", optional=True,
+        ("plugin_dir", StringSpec(default="./shepherd-plugins", optional=True,
                                   helptext="Optional directory for Shepherd to look for"
                                   " plugins in.")),
-        ("root_dir", StringSpec(default="~/shepherd", optional=True,
+        ("root_dir", StringSpec(default="./shepherd", optional=False,
                                 helptext="Operating directory for shepherd to place"
                                 " working files.")),
         ("custom_config_path", StringSpec(optional=True, helptext="Path to custom config"
@@ -294,11 +298,22 @@ def core_confspec():
 def resolve_core_conf_paths(core_conf):
     """
     Set the cwd to ``root_dir`` and resolve other core config paths relative to that.
-    Also expands out any "~" user characters.
+    ``root_dir`` itself will resolve relative to ``relative_dir``, intended to be the config
+    file directory.
+    Also expands out any "~" user characters. If paths are empty, leaves them as is, rather than
+     the default pathlib behaviour of resolving to the current directory
     """
+    os.chdir(relative_dir)
     core_conf["root_dir"] = str(Path(core_conf["root_dir"]).expanduser().resolve())
+    try:
     os.chdir(core_conf["root_dir"])
+    except FileNotFoundError:
+        raise FileNotFoundError(F"Shepherd root operating directory '{core_conf['root_dir']}'"
+                                F" does not exist")
+
+    if core_conf["plugin_dir"]:
     core_conf["plugin_dir"] = str(Path(core_conf["plugin_dir"]).expanduser().resolve())
+    if core_conf["custom_config_path"]:
     core_conf["custom_config_path"] = str(
         Path(core_conf["custom_config_path"]).expanduser().resolve())
     core_conf["generated_config_path"] = str(