diff --git a/integration_test.sh b/integration_test.sh
index 878a23b..7cd4e07 100755
--- a/integration_test.sh
+++ b/integration_test.sh
@@ -4,93 +4,116 @@ set -ex
 
 dest=$(mktemp -d)
 
-./cram --help
+PATH="$PATH:$(realpath .)"
+PS4='+(${BASH_SOURCE}:${LINENO}): ${FUNCNAME[0]:+${FUNCNAME[0]}(): }'
 
-root="test/integration/"
+cram --help
+
+root="test/integration"
+
+function ,scrub() {
+    rm -rf "${dest}"/* .cram.log
+}
 
 # Should be able to list all packages
-./cram list "$root" | grep "packages.d/p1"
+cram list "${root}" | grep "packages.d/p1"
+,scrub
 
 # P3 depends on P1, should show up in the listing
-./cram list "$root" packages.d/p3 | grep "packages.d/p1"
+cram list "${root}" packages.d/p3 | grep "packages.d/p1"
+,scrub
 
 # P4 depends on P3, should show up in the listing
-./cram list "$root" packages.d/p4 | grep "packages.d/p3"
+cram list "${root}" packages.d/p4 | grep "packages.d/p3"
+,scrub
 
 # The default profile should depend on its subpackage
-./cram list "$root" profiles.d/default | grep "profiles.d/default/subpackage"
+cram list "${root}" profiles.d/default | grep "profiles.d/default/subpackage"
+,scrub
 
 # And the subpackage has a dep
-./cram list "$root" profiles.d/default/subpackage | grep "packages.d/p3"
+cram list "${root}" profiles.d/default/subpackage | grep "packages.d/p3"
+,scrub
 
 # Install one package
-./cram apply --no-optimize --require packages.d/p1 --execute "$root" "${dest}"
+cram apply --no-optimize --require packages.d/p1 --execute "${root}" "${dest}"
 [ -L "${dest}"/foo ]
-./cram state "$root" | grep "${dest}/foo"
-rm -r "${dest}"/*
+cram state "$root" | grep "${dest}/foo"
+,scrub
 
 # Install two transitively (legacy)
-./cram apply --no-optimize --require packages.d/p3 --execute "$root" "${dest}"
+cram apply --no-optimize --require packages.d/p3 --execute "${root}" "${dest}"
 [ -L "${dest}"/foo ]
 [ -L "${dest}"/bar ]
-./cram state "$root" | grep "${dest}/foo"
-./cram state "$root" | grep "${dest}/bar"
-rm -r "${dest}"/*
+cram state "$root" | grep "${dest}/foo"
+cram state "$root" | grep "${dest}/bar"
+,scrub
 
 # Install two transitively (current)
-./cram apply --no-optimize --require packages.d/p4 --execute "$root" "${dest}"
+cram apply --no-optimize --require packages.d/p4 --execute "${root}" "${dest}"
 [ -L "${dest}"/foo ]
 [ -L "${dest}"/bar ]
-rm -r "${dest}"/*
+,scrub
 
 # Install two transitively (current)
-./cram apply --no-optimize --require packages.d/p4 --execute "$root" "${dest}"
+cram apply --no-optimize --require packages.d/p4 --execute "${root}" "${dest}"
 [ -L "${dest}"/foo ]
 [ -L "${dest}"/bar ]
-rm -r "${dest}"/*
+,scrub
 
 # Install two transitively (current)
-./cram apply --no-optimize --require hosts.d/test --require profiles.d/default --execute "$root" "${dest}"
+cram apply --no-optimize --require hosts.d/test --require profiles.d/default --execute "${root}" "${dest}"
+tree "${dest}"
 [ -L "${dest}"/foo ]
 [ -L "${dest}"/bar ]
-rm -r "${dest}"/*
+,scrub
 
 # INSTALL scripts get run as-is
-./cram list "$root" packages.d/p5 | grep "packages.d/p5/INSTALL"
+cram list "${root}" packages.d/p5 | grep "packages.d/p5/INSTALL"
+,scrub
 
 # Inline scripts get pulled out repeatably
-./cram list "$root" packages.d/p6 | grep "b5bea41b6c623f7c09f1bf24dcae58ebab3c0cdd90ad966bc43a45b44867e12b"
+cram list "${root}" packages.d/p6 | grep "b5bea41b6c623f7c09f1bf24dcae58ebab3c0cdd90ad966bc43a45b44867e12b"
+,scrub
 
 # Inline scripts get pulled out repeatably, even from the list format
-./cram list "$root" packages.d/p7 | grep "b5bea41b6c623f7c09f1bf24dcae58ebab3c0cdd90ad966bc43a45b44867e12b"
+cram list "${root}" packages.d/p7 | grep "b5bea41b6c623f7c09f1bf24dcae58ebab3c0cdd90ad966bc43a45b44867e12b"
+,scrub
 
 # Test log-based optimization
-./cram apply --no-optimize --require packages.d/p4 --execute "$root" "${dest}"
+cram apply --no-optimize --require packages.d/p4 --execute "${root}" "${dest}"
 [ -L "${dest}"/foo ]
 [ -L "${dest}"/bar ]
 # These paths were already linked, they shouldn't be re-linked when optimizing.
-! ./cram apply --require packages.d/p4 --optimize --execute "$root" "${dest}" | grep "${dest}/foo"
-! ./cram apply --require packages.d/p4 --optimize --execute "$root" "${dest}" | grep "${dest}/bar"
-rm -r "${dest}"/*
+! cram apply --require packages.d/p4 --optimize --execute "${root}" "${dest}" | grep "${dest}/foo"
+! cram apply --require packages.d/p4 --optimize --execute "${root}" "${dest}" | grep "${dest}/bar"
+,scrub
 
 # Likewise, if we've exec'd this once we shouldn't do it again
-./cram apply --no-optimize --require packages.d/p5 --execute "$root" "${dest}"
-! ./cram apply --require packages.d/p5 --execute "$root" "${dest}" | grep "exec"
+cram apply --no-optimize --require packages.d/p5 --execute "${root}" "${dest}"
+! cram apply --require packages.d/p5 --execute "${root}" "${dest}" | grep "exec"
+,scrub
 
 # ... unless the user tells us to
-./cram apply --no-optimize --require packages.d/p5 --execute "$root" "${dest}"
-./cram apply --exec-always --require packages.d/p5 --execute "$root" "${dest}" | grep "exec"
+cram apply --no-optimize --require packages.d/p5 --execute "${root}" "${dest}"
+cram apply --exec-always --require packages.d/p5 --execute "${root}" "${dest}" | grep "exec"
+,scrub
 
 # If multiple packages provide the same _effective_ script, do it once
-./cram apply --require packages.d/p6 --require packages.d/p7 --execute "$root" "${dest}" | sort | uniq -c | grep "/tmp/stow/b5bea41b6c623f7c09f1bf24dcae58ebab3c0cdd90ad966bc43a45b44867e12b.sh" | grep "1 - exec"
+cram apply --require packages.d/p6 --require packages.d/p7 --execute "${root}" "${dest}" | sort | uniq -c | grep "/tmp/stow/b5bea41b6c623f7c09f1bf24dcae58ebab3c0cdd90ad966bc43a45b44867e12b.sh" | grep "1 - exec"
+,scrub
 
 # Test log-based cleanup
-./cram apply --require packages.d/p1 --require packages.d/p2 --execute "$root" "${dest}"
+cram apply --require packages.d/p1 --require packages.d/p2 --execute "${root}" "${dest}"
+cram apply --require packages.d/p1 --require packages.d/p2 --execute "${root}" "${dest}"
 [ -L "${dest}"/foo ]
 [ -L "${dest}"/bar ]
+,scrub
+
 # And how bar shouldn't be installed...
-./cram state test/
-./cram apply --require packages.d/p1 --execute "$root" "${dest}"
-./cram state test/
+cram state "${root}"
+cram apply --require packages.d/p1 --execute "${root}" "${dest}"
+cram state "${root}"
 [ -L "${dest}"/foo ]
 [ ! -L "${dest}"/bar ]
+,scrub
diff --git a/src/python/cram/__main__.py b/src/python/cram/__main__.py
index b2e22e3..6ed5097 100644
--- a/src/python/cram/__main__.py
+++ b/src/python/cram/__main__.py
@@ -1,11 +1,9 @@
 """Cram's entry point."""
 
-from itertools import chain
 import logging
 import os
 from pathlib import Path
 import pickle
-from pprint import pprint
 from typing import List, Optional, Union
 import re
 import platform
@@ -128,7 +126,7 @@ def load_packages(root: Path, roots) -> dict:
 
     packages = {}
     for r in roots.get("package", []):
-        r = Path(r)
+        r = root / r
         log.debug(f"Trying to load packages from {r}...")
         for p in r.glob("*"):
             name = str(p.relative_to(root))
@@ -136,7 +134,7 @@ def load_packages(root: Path, roots) -> dict:
 
     for r in roots.get("profile", []):
         # Add profiles, hosts which contain subpackages.
-        r = Path(r)
+        r = root / r
         log.debug(f"Trying to load profiles from {r}...")
         for mp_root in r.glob("*"):
             # First find all subpackages
@@ -181,7 +179,7 @@ def build_fs(
         log.warning("Loaded no packages!")
 
     requirements = list(prelude)
-    for r in list(requirements):
+    for r in requirements:
         try:
             for d in packages[r].requires():
                 if d not in requirements:
@@ -190,7 +188,7 @@ def build_fs(
             missing_require_handler(r, e)
             requirements.remove(r)
 
-    log.debug(f"Mapped requirements {prelude} to {requirements}")
+    log.info(f"Mapped requirements {prelude} to {requirements}")
     # Compute the topsort graph
     requirements_graph = {r: packages[r].requires() for r in requirements}
     fs = Vfs()
@@ -273,7 +271,6 @@ def scrub(old_fs: Vfs, new_fs: Vfs) -> Vfs:
 def configure(ctx, param, filename: Optional[Path]):
     if filename and filename.exists():
         ctx.default_map = {}
-        os.chdir(filename.parent)
         log.debug(f"Loading config from {filename}")
         cfg = toml.load(filename)
         assert cfg["cram"]["version"] >= 1
@@ -306,8 +303,6 @@ def configure(ctx, param, filename: Optional[Path]):
         if error:
             exit(1)
 
-    pprint(ctx.default_map)
-
 
 @click.group(invoke_without_command=True)
 @click.option(
@@ -363,12 +358,14 @@ def arg_require(*args, **kwargs):
 def arg_require_root(*args, **kwargs):
     return click.option(
         "--require-root",
-        type=(str, click.Choice(["profile", "package"])),
+        type=(click.Choice(["profile", "package"]), str),
         multiple=True,
-        default=[("profiles.d", "profile"), ("hosts.d", "profile"), ("packages.d", "package")],
-        callback=lambda ctx, param, pairs: groupby(
-            [(y, expandvars(x)) for x, y in pairs], first, second
-        ),
+        default=[
+            ("profile", "profiles.d"),
+            ("profile", "hosts.d"),
+            ("package", "packages.d"),
+        ],
+        callback=lambda ctx, param, pairs: groupby(pairs, first, second),
     )(*args, **kwargs)
 
 
@@ -376,6 +373,7 @@ def arg_missing_require(*args, **kwargs):
     return click.option(
         "--missing-require",
         type=click.Choice(["error", "warn", "ignore"]),
+        default="error",
         callback=lambda ctx, param, it: {
             "ignore": missing_require_ignore,
             "warn": missing_require_warn,
@@ -414,7 +412,8 @@ def do_apply(
     """The entry point of cram."""
 
     # Resolve the two input paths to absolutes
-    root = confdir.resolve()
+    root = confdir.resolve().absolute()
+    os.chdir(root)
     dest = destdir.resolve()
 
     if not root.is_dir():
@@ -464,7 +463,9 @@ def do_apply(
 @click.argument("requirements", nargs=-1, callback=handle_requires)
 def do_list(confdir, requirements, require_root, oneline):
     """List out packages, profiles, hosts and subpackages in the <confdir>."""
-    root = confdir.resolve()
+
+    root = confdir.resolve().absolute()
+    os.chdir(root)
     log.debug(f"confdir: {root}, roots: {require_root}, requirements: {requirements}")
 
     if not root.is_dir():
@@ -503,7 +504,9 @@ def do_list(confdir, requirements, require_root, oneline):
 @click.argument("confdir", type=Path, callback=handle_path_vars)
 def do_state(confdir, state_file):
     """List out the last `apply` state in the <confdir>/.cram.log or --state-file."""
-    root = confdir.resolve()
+
+    root = confdir.resolve().absolute()
+    os.chdir(root)
 
     if not root.is_dir():
         log.fatal(f"{confdir} does not exist!")
@@ -521,10 +524,11 @@ def do_state(confdir, state_file):
 @arg_require_root
 @click.argument("confdir", type=Path, callback=handle_path_vars)
 @click.argument("requirement", type=str, callback=handle_path_vars)
-def do_fmt(confdir, requirement, require_root):
+def do_fmt(confdir: Path, requirement, require_root):
     """Format the specified requirement to a canonical-ish representation."""
 
-    root = confdir.resolve()
+    root = confdir.resolve().absolute()
+    os.chdir(root)
 
     if not root.is_dir():
         log.fatal(f"{confdir} does not exist!")
@@ -571,9 +575,9 @@ exec_idempotent = true
 # Where to load requirements from, and the requirement type
 # Types: package, profile
 require_root = [
-  ["${PWD}/packages.d", "package"],
-  ["${PWD}/profiles.d", "profile"],
-  ["${PWD}/hosts.d", "profile"],
+  ["package", "${PWD}/packages.d"],
+  ["profile", "${PWD}/profiles.d"],
+  ["profile", "${PWD}/hosts.d"],
 ]
 # Choice([error, warn, ignore])
 missing_require = "error"
@@ -594,7 +598,7 @@ require = [
 
 if __name__ == "__main__" or 1:
     logging.basicConfig(
-        level=logging.DEBUG,
+        level=logging.INFO,
         format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
     )
 
diff --git a/test/integration/cram.toml b/test/integration/cram.toml
index c38d62c..7d54f9f 100644
--- a/test/integration/cram.toml
+++ b/test/integration/cram.toml
@@ -7,12 +7,12 @@ destdir = "${HOME}"
 state_file = "${PWD}/.cram.log"
 optimize = true
 exec_idempotent = true
-# Where to load requirements from
+# Where to load requirements from, and the requirement type
 # Types: package, profile
 require_root = [
-  ["${PWD}/packages.d", "package"],
-  ["${PWD}/profiles.d", "profile"],
-  ["${PWD}/hosts.d", "profile"],
+  ["package", "${PWD}/packages.d"],
+  ["profile", "${PWD}/profiles.d"],
+  ["profile", "${PWD}/hosts.d"],
 ]
 # Choice([error, warn, ignore])
 missing_require = "error"
@@ -20,8 +20,7 @@ missing_require = "error"
 [cram.task.apply]
 missing_require = "ignore"
 require = [
-#   "hosts.d/${FQDN}",
-#  "hosts.d/${HOSTNAME}",
-  "hosts.d/test",
+  "hosts.d/${FQDN}",
+  "hosts.d/${HOSTNAME}",
   "profiles.d/default",
 ]