diff --git a/assets/manifests/default b/assets/manifests/default
deleted file mode 100644
index eb76027..0000000
--- a/assets/manifests/default
+++ /dev/null
@@ -1,5 +0,0 @@
-kernel,kernel
-kernel,panic.serial
-user,drv.uefi_fb
-user,testapp
-user,srv.init
diff --git a/assets/manifests/default.yaml b/assets/manifests/default.yaml
new file mode 100644
index 0000000..2399b73
--- /dev/null
+++ b/assets/manifests/default.yaml
@@ -0,0 +1,8 @@
+---
+programs:
+  - name: panic.serial
+    target: kernel
+
+  - name: drv.uefi_fb
+  - name: testapp
+  - name: srv.init
diff --git a/configs/base.toml b/configs/base.yaml
similarity index 78%
rename from configs/base.toml
rename to configs/base.yaml
index df3e4f3..4d917bc 100644
--- a/configs/base.toml
+++ b/configs/base.yaml
@@ -1,13 +1,14 @@
-[variables]
-cc = "clang"
-cxx = "clang++"
-ld = "ld.lld"
-ar = "ar"
-nasm = "nasm"
-objcopy = "objcopy"
-cog = "cog"
+---
+variables:
+  cc: clang
+  cxx: clang++
+  ld: ld.lld
+  ar: ar
+  nasm: nasm
+  objcopy: objcopy
+  cog: cog
 
-ccflags = [
+  ccflags: [
     "-I${source_root}/src/include",
     "-I${source_root}/src/include/x86_64",
     "-fcolor-diagnostics",
@@ -17,27 +18,25 @@ ccflags = [
     "-DVERSION_GITSHA=0x${version_sha}",
     '-DGIT_VERSION=\"${version_major}.${version_minor}.${version_patch}+${version_sha}\"',
     '-DGIT_VERSION_WIDE=L\"${version_major}.${version_minor}.${version_patch}+${version_sha}\"',
+
     "-Wformat=2", "-Winit-self", "-Wfloat-equal", "-Winline", "-Wmissing-format-attribute",
     "-Wmissing-include-dirs", "-Wswitch", "-Wundef", "-Wdisabled-optimization",
     "-Wpointer-arith", "-Wno-attributes", "-Wno-sign-compare", "-Wno-multichar",
     "-Wno-div-by-zero", "-Wno-endif-labels", "-Wno-pragmas", "-Wno-format-extra-args",
     "-Wno-unused-result", "-Wno-deprecated-declarations", "-Wno-unused-function",
-    "-Wno-address-of-packed-member", "-Wno-invalid-offsetof", "-Werror",
-]
+    "-Wno-address-of-packed-member", "-Wno-invalid-offsetof", "-Werror" ]
 
-asflags = [
+  asflags: [
     "-DVERSION_MAJOR=${version_major}",
     "-DVERSION_MINOR=${version_minor}",
     "-DVERSION_PATCH=${version_patch}",
     "-DVERSION_GITSHA=0x${version_sha}",
-    "-I${source_root}/src/include",
-]
+    "-I${source_root}/src/include" ]
 
-cflags = ["-std=c11"]
-cxxflags = ["-std=c++17"]
+  cflags: [ "-std=c11" ]
+  cxxflags: [ "-std=c++17" ]
 
-cogflags = [
+  cogflags: [
     "-I", "${source_root}/scripts",
-    "-D", "definitions_path=${source_root}/definitions"
-]
+    "-D", "definitions_path=${source_root}/definitions" ]
 
diff --git a/configs/boot-debug.toml b/configs/boot-debug.yaml
similarity index 64%
rename from configs/boot-debug.toml
rename to configs/boot-debug.yaml
index 3da0a15..507abe0 100644
--- a/configs/boot-debug.toml
+++ b/configs/boot-debug.yaml
@@ -1,10 +1,10 @@
-extends = "base"
+---
+extends: base
 
-[variables]
+variables:
+  ld: clang++
 
-ld = "clang++"
-
-ccflags = [
+  ccflags: [
     "-I${source_root}/external",
     "--target=x86_64-unknown-windows",
     "-ffreestanding",
@@ -13,23 +13,15 @@ ccflags = [
     "-fno-omit-frame-pointer",
     "-ggdb",
     "-g3",
-    '-DKERNEL_FILENAME=L"jsix.elf"',
-]
+    '-DKERNEL_FILENAME=L"jsix.elf"' ]
 
+  cxxflags: [ "-fno-exceptions", "-fno-rtti" ]
 
-cflags = [
-]
-
-cxxflags = [
-    "-fno-exceptions",
-    "-fno-rtti",
-]
-
-ldflags = [
+  ldflags: [
     "--target=x86_64-unknown-windows",
     "-nostdlib",
     "-Wl,-entry:efi_main",
     "-Wl,-subsystem:efi_application",
     "-fuse-ld=lld-link",
-    "-g"
-]
+    "-g" ]
+
diff --git a/configs/kernel-debug.toml b/configs/kernel-debug.yaml
similarity index 64%
rename from configs/kernel-debug.toml
rename to configs/kernel-debug.yaml
index 9358dde..3781aec 100644
--- a/configs/kernel-debug.toml
+++ b/configs/kernel-debug.yaml
@@ -1,47 +1,47 @@
-extends = "base"
+---
+extends: base
 
-[variables]
-asflags = [ 
-    "-I${source_root}/src/kernel/",
-]
+variables:
+  asflags: [ "-I${source_root}/src/kernel/" ]
 
-ccflags = [
+  ccflags: [
     "--target=x86_64-unknown-elf",
     "-I${source_root}/external",
+
     "-nostdlib",
     "-ffreestanding",
     "-nodefaultlibs",
     "-fno-builtin",
+
     "-mno-sse",
     "-fno-omit-frame-pointer",
     "-mno-red-zone",
-    "-g",
     "-mcmodel=large",
+
+    "-g",
+
     "-D__ELF__",
     "-D__JSIX__",
-    "-isystem${source_root}/sysroot/include",
-    "-isystem${source_root}/src/libraries/libc/include",
-    "--sysroot='${source_root}/sysroot'",
     "-U__linux",
     "-U__linux__",
-]
 
-cflags = [
-    '-nostdinc',
-]
+    "-isystem${source_root}/sysroot/include",
+    "-isystem${source_root}/src/libraries/libc/include",
+    "--sysroot='${source_root}/sysroot'" ]
 
-cxxflags = [
+
+  cflags: [ '-nostdinc' ]
+
+  cxxflags: [
     "-fno-exceptions",
     "-fno-rtti",
-    '-nostdinc',
-    "-isystem${source_root}/sysroot/include/c++/v1"
-]
+    "-nostdinc",
+    "-isystem${source_root}/sysroot/include/c++/v1" ]
 
-ldflags = [
+  ldflags: [
     "-g",
     "-nostdlib",
     "-Bstatic",
     "-z", "norelro",
-    "-z", "separate-code",
-]
+    "-z", "separate-code" ]
 
diff --git a/configs/user-debug.toml b/configs/user-debug.yaml
similarity index 61%
rename from configs/user-debug.toml
rename to configs/user-debug.yaml
index a8d882d..ae2d9ab 100644
--- a/configs/user-debug.toml
+++ b/configs/user-debug.yaml
@@ -1,34 +1,34 @@
-extends = "base"
+---
+extends: base
 
-[variables]
-asflags = [
-    "-I${source_root}/src/kernel/",
-]
+variables:
+  asflags: [ "-I${source_root}/src/kernel/" ]
 
-ccflags = [
+  ccflags: [
     "-mno-sse",
     "-fno-omit-frame-pointer",
+
     "-g",
+
     "-D__ELF__",
     "-D__JSIX__",
-    "-isystem${source_root}/sysroot/include",
-    "-isystem${source_root}/src/libraries/libc/include",
-    "--sysroot='${source_root}/sysroot'",
     "-U__linux",
     "-U__linux__",
-]
 
-cxxflags = [
+    "-isystem${source_root}/sysroot/include",
+    "-isystem${source_root}/src/libraries/libc/include",
+    "--sysroot='${source_root}/sysroot'" ]
+
+
+  cxxflags: [
     "-fno-exceptions",
     "-fno-rtti",
-    "-isystem${source_root}/sysroot/include/c++/v1"
-]
+    "-isystem${source_root}/sysroot/include/c++/v1" ]
 
-ldflags = [
+  ldflags: [
     "-g",
     "-Bstatic",
     "--sysroot='${source_root}/sysroot'",
     "-L", "${source_root}/sysroot/lib",
-    "-z", "separate-code",
-]
+    "-z", "separate-code" ]
 
diff --git a/configure b/configure
index 2576255..4ba5ff9 100755
--- a/configure
+++ b/configure
@@ -47,7 +47,7 @@ if __name__ == "__main__":
     from bonnibel import BonnibelError
 
     p = ArgumentParser(description="Generate jsix build files")
-    p.add_argument("--manifest", "-m", metavar="FILE", default="assets/manifests/default",
+    p.add_argument("--manifest", "-m", metavar="FILE", default="assets/manifests/default.yaml",
             help="File to use as the system manifest")
     p.add_argument("--config", "-c", metavar="NAME", default="debug",
             help="Configuration to build (eg, 'debug' or 'release')")
diff --git a/requirements.txt b/requirements.txt
index 10f8055..6cb549a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
 cogapp >= 3
 ninja >= 1.10.2
 peru >= 1.2.1
-toml >= 0.10.2
+pyyaml >= 5.4
diff --git a/scripts/bonnibel/__init__.py b/scripts/bonnibel/__init__.py
index 337ec82..1ba3953 100644
--- a/scripts/bonnibel/__init__.py
+++ b/scripts/bonnibel/__init__.py
@@ -1,3 +1,8 @@
 class BonnibelError(Exception):
     def __init__(self, message):
         self.message = message
+
+def load_config(filename):
+    from yaml import safe_load
+    with open(filename, 'r') as infile:
+        return safe_load(infile.read())
diff --git a/scripts/bonnibel/project.py b/scripts/bonnibel/project.py
index da72207..a995ae0 100644
--- a/scripts/bonnibel/project.py
+++ b/scripts/bonnibel/project.py
@@ -10,11 +10,12 @@ class Project:
     def __str__(self):
         return f"{self.name} {self.version.major}.{self.version.minor}.{self.version.patch}-{self.version.sha}"
 
-    def generate(self, root, output, modules, config, manifest):
+    def generate(self, root, output, modules, config, manifest_file):
         import sys
         import bonnibel
         from os.path import join
         from ninja.ninja_syntax import Writer
+        from . import load_config
         from .target import Target
 
         targets = set()
@@ -47,11 +48,7 @@ class Project:
             fatroot.mkdir(exist_ok=True)
 
             fatroot_content = []
-            for line in open(manifest, 'r'):
-                target, name = line.split(",", 1)
-                target = target.strip()
-                name = name.strip()
-
+            def add_fatroot(name, target):
                 if not name in modules:
                     raise BonnibelError(f"Manifest item '{name}' is not a known module")
 
@@ -66,9 +63,23 @@ class Project:
                         "name": f"Installing {name}",
                         "debug": f"${{build_root}}/{mod.output}.debug",
                     })
+
                 fatroot_content.append(fatroot_output)
                 build.newline()
 
+            manifest = load_config(manifest_file)
+            programs = manifest.get("programs", tuple())
+
+            kernel = manifest.get("kernel", dict())
+            add_fatroot(
+                kernel.get("name", "kernel"),
+                kernel.get("target", "kernel"))
+
+            for program in programs:
+                name = program["name"]
+                target = program.get("target", "user")
+                add_fatroot(name, target)
+
             symbol_table = "${build_root}/fatroot/symbol_table.dat"
             build.build(
                 rule = "makest",
@@ -123,7 +134,7 @@ class Project:
             build.newline()
 
             regen_implicits = \
-                [f"{self.root}/configure", str(manifest)] + \
+                [f"{self.root}/configure", str(manifest_file)] + \
                 [str(mod.modfile) for mod in modules.values()]
 
             for target in targets:
diff --git a/scripts/bonnibel/target.py b/scripts/bonnibel/target.py
index 8d3e8b4..30a076b 100644
--- a/scripts/bonnibel/target.py
+++ b/scripts/bonnibel/target.py
@@ -3,7 +3,7 @@ class Target(dict):
 
     @classmethod
     def load(cls, root, name, config=None):
-        import toml
+        from . import load_config
 
         if (name, config) in cls.__targets:
             return cls.__targets[(name, config)]
@@ -17,9 +17,9 @@ class Target(dict):
             basename += f"-{config}"
 
         while basename is not None:
-            filename = str(configs / (basename + ".toml"))
+            filename = str(configs / (basename + ".yaml"))
             depfiles.append(filename)
-            desc = toml.load(filename)
+            desc = load_config(filename)
             basename = desc.get("extends")
             dicts.append(desc.get("variables", dict()))