diff --git a/cmd/quill/cli/cli.go b/cmd/quill/cli/cli.go
index a026dc7..2b2b919 100644
--- a/cmd/quill/cli/cli.go
+++ b/cmd/quill/cli/cli.go
@@ -38,9 +38,9 @@ func New(id clio.Identification) *cobra.Command {
 			},
 		)
 
-	app := clio.New(*clioCfg)
+	root := &cobra.Command{}
 
-	root := app.SetupCommand(&cobra.Command{})
+	app := clio.New(*clioCfg, root)
 
 	submission := commands.Submission(app)
 	submission.AddCommand(commands.SubmissionList(app))
@@ -54,7 +54,7 @@ func New(id clio.Identification) *cobra.Command {
 	p12.AddCommand(commands.P12AttachChain(app))
 	p12.AddCommand(commands.P12Describe(app))
 
-	root.AddCommand(clio.VersionCommand(app))
+	root.AddCommand(clio.VersionCommand(id))
 	root.AddCommand(commands.Sign(app))
 	root.AddCommand(commands.Notarize(app))
 	root.AddCommand(commands.SignAndNotarize(app))
diff --git a/cmd/quill/cli/commands/describe.go b/cmd/quill/cli/commands/describe.go
index 64bf5a9..dce8b27 100644
--- a/cmd/quill/cli/commands/describe.go
+++ b/cmd/quill/cli/commands/describe.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"fmt"
 	"strings"
 
@@ -42,7 +41,7 @@ func Describe(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			var err error
@@ -63,6 +62,6 @@ func Describe(app clio.Application) *cobra.Command {
 			bus.Report(buf.String())
 
 			return nil
-		}),
+		},
 	}, opts)
 }
diff --git a/cmd/quill/cli/commands/embedded_certificates.go b/cmd/quill/cli/commands/embedded_certificates.go
index 2960dcb..356777b 100644
--- a/cmd/quill/cli/commands/embedded_certificates.go
+++ b/cmd/quill/cli/commands/embedded_certificates.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"fmt"
 	"io"
 	"strings"
@@ -21,7 +20,7 @@ func EmbeddedCerts(app clio.Application) *cobra.Command {
 		Use:   "embedded-certificates",
 		Short: "show the certificates embedded into quill (typically the Apple root and intermediate certs)",
 		Args:  cobra.NoArgs,
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			var err error
@@ -36,7 +35,7 @@ func EmbeddedCerts(app clio.Application) *cobra.Command {
 			bus.Report(buf.String())
 
 			return nil
-		}),
+		},
 	})
 }
 
diff --git a/cmd/quill/cli/commands/extract_certificates.go b/cmd/quill/cli/commands/extract_certificates.go
index 3347b28..cea7906 100644
--- a/cmd/quill/cli/commands/extract_certificates.go
+++ b/cmd/quill/cli/commands/extract_certificates.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"encoding/pem"
 	"strings"
 
@@ -41,7 +40,7 @@ func ExtractCertificates(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			certs, err := extractCertificates(opts.Path, opts.Leaf)
@@ -53,7 +52,7 @@ func ExtractCertificates(app clio.Application) *cobra.Command {
 			bus.Notify("Try running 'openssl x509 -text -in <path-to-file-with-output>.pem' to view the certificate details")
 
 			return nil
-		}),
+		},
 	}, opts)
 }
 
diff --git a/cmd/quill/cli/commands/notarize.go b/cmd/quill/cli/commands/notarize.go
index 415d9e0..55b73b3 100644
--- a/cmd/quill/cli/commands/notarize.go
+++ b/cmd/quill/cli/commands/notarize.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"time"
 
 	"github.com/spf13/cobra"
@@ -48,7 +47,7 @@ func Notarize(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			// TODO: verify path is a signed darwin binary
@@ -59,7 +58,7 @@ func Notarize(app clio.Application) *cobra.Command {
 			}
 			_, err := notarize(opts.Path, opts.Notary, opts.Status)
 			return err
-		}),
+		},
 	}, opts)
 }
 
diff --git a/cmd/quill/cli/commands/p12_attach_chain.go b/cmd/quill/cli/commands/p12_attach_chain.go
index 7d1fec1..dc0851d 100644
--- a/cmd/quill/cli/commands/p12_attach_chain.go
+++ b/cmd/quill/cli/commands/p12_attach_chain.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"crypto/rand"
 	"crypto/x509"
 	"fmt"
@@ -54,7 +53,7 @@ func P12AttachChain(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			newFilename, err := writeP12WithChain(opts.Path, opts.P12.Password, opts.Keychain.Path, true)
@@ -71,7 +70,7 @@ func P12AttachChain(app clio.Application) *cobra.Command {
 			bus.Notify(fmt.Sprintf("Wrote new p12 file with certificate chain to %q", newFilename))
 
 			return nil
-		}),
+		},
 	}, opts)
 }
 
diff --git a/cmd/quill/cli/commands/p12_describe.go b/cmd/quill/cli/commands/p12_describe.go
index d1c5542..cd00b00 100644
--- a/cmd/quill/cli/commands/p12_describe.go
+++ b/cmd/quill/cli/commands/p12_describe.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"crypto/x509"
 	"fmt"
 	"reflect"
@@ -37,7 +36,7 @@ func P12Describe(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			description, err := describeP12(opts.Path, opts.Password)
@@ -48,7 +47,7 @@ func P12Describe(app clio.Application) *cobra.Command {
 			bus.Report(description)
 
 			return nil
-		}),
+		},
 	}, opts)
 }
 
diff --git a/cmd/quill/cli/commands/sign.go b/cmd/quill/cli/commands/sign.go
index 7e10e45..3f7f0b7 100644
--- a/cmd/quill/cli/commands/sign.go
+++ b/cmd/quill/cli/commands/sign.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"fmt"
 
 	"github.com/spf13/cobra"
@@ -38,11 +37,11 @@ func Sign(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			return sign(opts.Path, opts.Signing)
-		}),
+		},
 	}, opts)
 }
 
diff --git a/cmd/quill/cli/commands/sign_and_notarize.go b/cmd/quill/cli/commands/sign_and_notarize.go
index 3270501..822ab20 100644
--- a/cmd/quill/cli/commands/sign_and_notarize.go
+++ b/cmd/quill/cli/commands/sign_and_notarize.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"fmt"
 
 	"github.com/spf13/cobra"
@@ -48,7 +47,7 @@ func SignAndNotarize(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			err := sign(opts.Path, opts.Signing)
@@ -67,6 +66,6 @@ func SignAndNotarize(app clio.Application) *cobra.Command {
 			}
 
 			return nil
-		}),
+		},
 	}, opts)
 }
diff --git a/cmd/quill/cli/commands/submission_list.go b/cmd/quill/cli/commands/submission_list.go
index aff01fe..439d2e2 100644
--- a/cmd/quill/cli/commands/submission_list.go
+++ b/cmd/quill/cli/commands/submission_list.go
@@ -25,7 +25,7 @@ func SubmissionList(app clio.Application) *cobra.Command {
 		Use:   "list",
 		Short: "list previous submissions to Apple's Notary service",
 		Args:  cobra.NoArgs,
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			log.Info("fetching previous submissions")
@@ -64,6 +64,6 @@ func SubmissionList(app clio.Application) *cobra.Command {
 			bus.Report(t.Render())
 
 			return nil
-		}),
+		},
 	}, opts)
 }
diff --git a/cmd/quill/cli/commands/submission_logs.go b/cmd/quill/cli/commands/submission_logs.go
index 3dae98a..cbc06c5 100644
--- a/cmd/quill/cli/commands/submission_logs.go
+++ b/cmd/quill/cli/commands/submission_logs.go
@@ -1,8 +1,6 @@
 package commands
 
 import (
-	"context"
-
 	"github.com/spf13/cobra"
 
 	"github.com/anchore/clio"
@@ -36,7 +34,7 @@ func SubmissionLogs(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			log.Infof("fetching submission logs for %q", opts.ID)
@@ -56,7 +54,7 @@ func SubmissionLogs(app clio.Application) *cobra.Command {
 
 			sub := notary.ExistingSubmission(a, opts.ID)
 
-			content, err := sub.Logs(ctx)
+			content, err := sub.Logs(cmd.Context())
 			if err != nil {
 				return err
 			}
@@ -64,6 +62,6 @@ func SubmissionLogs(app clio.Application) *cobra.Command {
 			bus.Report(content)
 
 			return nil
-		}),
+		},
 	}, opts)
 }
diff --git a/cmd/quill/cli/commands/submission_status.go b/cmd/quill/cli/commands/submission_status.go
index bb15dbd..0b52549 100644
--- a/cmd/quill/cli/commands/submission_status.go
+++ b/cmd/quill/cli/commands/submission_status.go
@@ -1,7 +1,6 @@
 package commands
 
 import (
-	"context"
 	"time"
 
 	"github.com/spf13/cobra"
@@ -42,7 +41,7 @@ func SubmissionStatus(app clio.Application) *cobra.Command {
 				return nil
 			},
 		),
-		RunE: app.Run(func(ctx context.Context) error {
+		RunE: func(cmd *cobra.Command, args []string) error {
 			defer bus.Exit()
 
 			log.Infof("checking submission status for %q", opts.ID)
@@ -70,9 +69,9 @@ func SubmissionStatus(app clio.Application) *cobra.Command {
 
 			var status notary.SubmissionStatus
 			if opts.Wait {
-				status, err = notary.PollStatus(ctx, sub, cfg.StatusConfig)
+				status, err = notary.PollStatus(cmd.Context(), sub, cfg.StatusConfig)
 			} else {
-				status, err = sub.Status(ctx)
+				status, err = sub.Status(cmd.Context())
 			}
 			if err != nil {
 				return err
@@ -81,6 +80,6 @@ func SubmissionStatus(app clio.Application) *cobra.Command {
 			bus.Report(string(status))
 
 			return nil
-		}),
+		},
 	}, opts)
 }