diff --git a/Makefile b/Makefile
index b17906b..4107aed 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,8 @@
 SHELL := /bin/bash
 
 build:
-	go build -v -o pal ./cmd
+	go build -v -o pal ./
+	chmod +rwx ./pal
 
 run:
-	go run ./cmd/
+	go run ./
diff --git a/cmd/main.go b/cmd/main.go
deleted file mode 100644
index d8fa929..0000000
--- a/cmd/main.go
+++ /dev/null
@@ -1,7 +0,0 @@
-package main
-
-import "fmt"
-
-func main() {
-	fmt.Println("hello")
-}
diff --git a/cmd/root.go b/cmd/root.go
new file mode 100644
index 0000000..17d1546
--- /dev/null
+++ b/cmd/root.go
@@ -0,0 +1,150 @@
+package cmd
+
+import (
+	"fmt"
+	"os"
+
+	"github.com/mobyvb/pull-pal/pullpal"
+	"github.com/mobyvb/pull-pal/vc"
+	"github.com/spf13/cobra"
+	"github.com/spf13/viper"
+	"go.uber.org/zap"
+)
+
+// rootCmd represents the base command when called without any subcommands
+var rootCmd = &cobra.Command{
+	Use:   "pull-pal",
+	Short: "A bot that uses large language models to act as a collaborator on a git project",
+	Long: `A bot that uses large language models to act as a collaborator on a git project.
+
+It can be used to:
+* Monitor a repository for open issues, and generate LLM prompts according to the issue details
+* Read an LLM response and process it into a new git commit and code change request on the version control server
+`,
+	// Uncomment the following line if your bare application
+	// has an action associated with it:
+	Run: func(cmd *cobra.Command, args []string) {
+		selfHandle := viper.GetString("handle")
+		selfEmail := viper.GetString("email")
+		repoDomain := viper.GetString("repo-domain")
+		repoHandle := viper.GetString("repo-handle")
+		repoName := viper.GetString("repo-name")
+		githubToken := viper.GetString("github-token")
+		localRepoPath := viper.GetString("local-repo-path")
+		promptPath := viper.GetString("prompt-path")
+		responsePath := viper.GetString("response-path")
+
+		log, err := zap.NewProduction()
+		if err != nil {
+			panic(err)
+		}
+
+		author := vc.Author{
+			Email:  selfEmail,
+			Handle: selfHandle,
+			Token:  githubToken,
+		}
+		repo := vc.Repository{
+			LocalPath:  localRepoPath,
+			HostDomain: repoDomain,
+			Name:       repoName,
+			Owner: vc.Author{
+				Handle: repoHandle,
+			},
+		}
+		p, err := pullpal.NewPullPal(cmd.Context(), log.Named("pullpal"), author, repo)
+		if err != nil {
+			log.Error("error creating new pull pal", zap.Error(err))
+			return
+		}
+		log.Info("Successfully initialized pull pal")
+
+		issue, changeRequest, err := p.PickIssueToFile(promptPath)
+		if err != nil {
+			log.Error("error selecting issue and/or generating prompt", zap.Error(err))
+			return
+		}
+
+		log.Info("Picked issue and created prompt", zap.String("issue ID", issue.ID), zap.String("prompt location", promptPath))
+
+		log.Info("Insert LLM response into response file", zap.String("response location", responsePath))
+
+		var input string
+		log.Info("Press 'enter' when done.")
+		fmt.Scanln(&input)
+
+		prURL, err := p.ProcessResponseFromFile(changeRequest, responsePath)
+		if err != nil {
+			log.Error("error parsing LLM response and/or making version control changes", zap.Error(err))
+			return
+		}
+
+		log.Info("Successfully opened a code change request", zap.String("Github PR link", prURL))
+	},
+}
+
+// Execute adds all child commands to the root command and sets flags appropriately.
+// This is called by main.main(). It only needs to happen once to the rootCmd.
+func Execute() {
+	err := rootCmd.Execute()
+	if err != nil {
+		os.Exit(1)
+	}
+}
+
+var cfgFile string
+
+func init() {
+	cobra.OnInitialize(initConfig)
+
+	// TODO make config values requried
+	rootCmd.PersistentFlags().StringVar(&cfgFile, "config", "", "config file (default is $HOME/.pull-pal.yaml)")
+
+	rootCmd.PersistentFlags().StringP("handle", "u", "HANDLE", "handle to use for version control actions")
+	rootCmd.PersistentFlags().StringP("email", "e", "EMAIL", "email to use for version control actions")
+	rootCmd.PersistentFlags().StringP("repo-domain", "d", "github.com", "domain for version control server")
+	rootCmd.PersistentFlags().StringP("repo-handle", "o", "REPO-HANDLE", "handle of repository's owner on version control server")
+	rootCmd.PersistentFlags().StringP("repo-name", "n", "REPO-NAME", "name of repository on version control server")
+	rootCmd.PersistentFlags().StringP("github-token", "t", "GITHUB TOKEN", "token for authenticating Github actions")
+	rootCmd.PersistentFlags().StringP("local-repo-path", "l", "/tmp/pullpalrepo/", "path where pull pal will check out a local copy of the repository")
+	rootCmd.PersistentFlags().StringP("prompt-path", "p", "./path/to/prompt.txt", "path where pull pal will write the llm prompt")
+	rootCmd.PersistentFlags().StringP("response-path", "r", "./path/to/response.txt", "path where pull pal will read the llm response from")
+
+	viper.BindPFlag("handle", rootCmd.PersistentFlags().Lookup("handle"))
+	viper.BindPFlag("email", rootCmd.PersistentFlags().Lookup("email"))
+	viper.BindPFlag("repo-domain", rootCmd.PersistentFlags().Lookup("repo-domain"))
+	viper.BindPFlag("repo-handle", rootCmd.PersistentFlags().Lookup("repo-handle"))
+	viper.BindPFlag("repo-name", rootCmd.PersistentFlags().Lookup("repo-name"))
+	viper.BindPFlag("github-token", rootCmd.PersistentFlags().Lookup("github-token"))
+	viper.BindPFlag("local-repo-path", rootCmd.PersistentFlags().Lookup("local-repo-path"))
+	viper.BindPFlag("prompt-path", rootCmd.PersistentFlags().Lookup("prompt-path"))
+	viper.BindPFlag("response-path", rootCmd.PersistentFlags().Lookup("response-path"))
+}
+
+func initConfig() {
+	fmt.Println("init")
+	if cfgFile != "" {
+		fmt.Println("cfg file exists")
+		// Use config file from the flag.
+		viper.SetConfigFile(cfgFile)
+	} else {
+		fmt.Println("cfg file empty")
+		// Find home directory.
+		home, err := os.UserHomeDir()
+		cobra.CheckErr(err)
+
+		// Search config in home directory with name ".cobra" (without extension).
+		viper.AddConfigPath(home)
+		viper.SetConfigType("yaml")
+		viper.SetConfigName(".pull-pal")
+	}
+
+	// TODO figure out how to get env variables to work
+	viper.SetEnvPrefix("pullpal")
+	viper.AutomaticEnv()
+
+	if err := viper.ReadInConfig(); err == nil {
+		fmt.Println("Using config file:", viper.ConfigFileUsed())
+	}
+
+}
diff --git a/go.mod b/go.mod
index 7db73f5..96bd074 100644
--- a/go.mod
+++ b/go.mod
@@ -5,6 +5,8 @@ go 1.20
 require (
 	github.com/go-git/go-git/v5 v5.6.1
 	github.com/google/go-github v17.0.0+incompatible
+	github.com/spf13/cobra v1.7.0
+	github.com/spf13/viper v1.15.0
 	go.uber.org/zap v1.24.0
 	golang.org/x/oauth2 v0.7.0
 )
@@ -15,23 +17,37 @@ require (
 	github.com/acomagu/bufpipe v1.0.4 // indirect
 	github.com/cloudflare/circl v1.1.0 // indirect
 	github.com/emirpasic/gods v1.18.1 // indirect
+	github.com/fsnotify/fsnotify v1.6.0 // indirect
 	github.com/go-git/gcfg v1.5.0 // indirect
 	github.com/go-git/go-billy/v5 v5.4.1 // indirect
 	github.com/golang/protobuf v1.5.2 // indirect
 	github.com/google/go-querystring v1.1.0 // indirect
+	github.com/hashicorp/hcl v1.0.0 // indirect
 	github.com/imdario/mergo v0.3.13 // indirect
+	github.com/inconshreveable/mousetrap v1.1.0 // indirect
 	github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
 	github.com/kevinburke/ssh_config v1.2.0 // indirect
+	github.com/magiconair/properties v1.8.7 // indirect
+	github.com/mitchellh/mapstructure v1.5.0 // indirect
+	github.com/pelletier/go-toml/v2 v2.0.6 // indirect
 	github.com/pjbgf/sha1cd v0.3.0 // indirect
 	github.com/sergi/go-diff v1.1.0 // indirect
 	github.com/skeema/knownhosts v1.1.0 // indirect
+	github.com/spf13/afero v1.9.3 // indirect
+	github.com/spf13/cast v1.5.0 // indirect
+	github.com/spf13/jwalterweatherman v1.1.0 // indirect
+	github.com/spf13/pflag v1.0.5 // indirect
+	github.com/subosito/gotenv v1.4.2 // indirect
 	github.com/xanzy/ssh-agent v0.3.3 // indirect
-	go.uber.org/atomic v1.7.0 // indirect
-	go.uber.org/multierr v1.6.0 // indirect
+	go.uber.org/atomic v1.9.0 // indirect
+	go.uber.org/multierr v1.8.0 // indirect
 	golang.org/x/crypto v0.6.0 // indirect
 	golang.org/x/net v0.9.0 // indirect
 	golang.org/x/sys v0.7.0 // indirect
+	golang.org/x/text v0.9.0 // indirect
 	google.golang.org/appengine v1.6.7 // indirect
-	google.golang.org/protobuf v1.28.0 // indirect
+	google.golang.org/protobuf v1.28.1 // indirect
+	gopkg.in/ini.v1 v1.67.0 // indirect
 	gopkg.in/warnings.v0 v0.1.2 // indirect
+	gopkg.in/yaml.v3 v3.0.1 // indirect
 )
diff --git a/go.sum b/go.sum
index f91ed84..c7744a6 100644
--- a/go.sum
+++ b/go.sum
@@ -1,3 +1,43 @@
+cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
+cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
+cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU=
+cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU=
+cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY=
+cloud.google.com/go v0.44.3/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY=
+cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc=
+cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0=
+cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To=
+cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4=
+cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6M=
+cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc=
+cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKVk=
+cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs=
+cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOYc=
+cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY=
+cloud.google.com/go v0.72.0/go.mod h1:M+5Vjvlc2wnp6tjzE102Dw08nGShTscUx2nZMufOKPI=
+cloud.google.com/go v0.74.0/go.mod h1:VV1xSbzvo+9QJOxLDaJfTjx5e+MePCpCWwvftOeQmWk=
+cloud.google.com/go v0.75.0/go.mod h1:VGuuCn7PG0dwsd5XPVm2Mm3wlh3EL55/79EKB6hlPTY=
+cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o=
+cloud.google.com/go/bigquery v1.3.0/go.mod h1:PjpwJnslEMmckchkHFfq+HTD2DmtT67aNFKH1/VBDHE=
+cloud.google.com/go/bigquery v1.4.0/go.mod h1:S8dzgnTigyfTmLBfrtrhyYhwRxG72rYxvftPBK2Dvzc=
+cloud.google.com/go/bigquery v1.5.0/go.mod h1:snEHRnqQbz117VIFhE8bmtwIDY80NLUZUMb4Nv6dBIg=
+cloud.google.com/go/bigquery v1.7.0/go.mod h1://okPTzCYNXSlb24MZs83e2Do+h+VXtc4gLoIoXIAPc=
+cloud.google.com/go/bigquery v1.8.0/go.mod h1:J5hqkt3O0uAFnINi6JXValWIb1v0goeZM77hZzJN/fQ=
+cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE=
+cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk=
+cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I=
+cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw=
+cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA=
+cloud.google.com/go/pubsub v1.3.1/go.mod h1:i+ucay31+CNRpDW4Lu78I4xXG+O1r/MAHgjpRVR+TSU=
+cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiyrjsg+URw=
+cloud.google.com/go/storage v1.5.0/go.mod h1:tpKbwo567HUNpVclU5sGELwQWBDZ8gh0ZeosJ0Rtdos=
+cloud.google.com/go/storage v1.6.0/go.mod h1:N7U0C8pVQ/+NIKOBQyamJIeKQKkZ+mxpohlUTyfDhBk=
+cloud.google.com/go/storage v1.8.0/go.mod h1:Wv1Oy7z6Yz3DshWRJFhqM/UCfaWIRTdp0RXyy7KQOVs=
+cloud.google.com/go/storage v1.10.0/go.mod h1:FLPqc6j+Ki4BU591ie1oL6qBQGu2Bl/tZ9ullr3+Kg0=
+cloud.google.com/go/storage v1.14.0/go.mod h1:GrKmX003DSIwi9o29oFT7YDnHYwZoctc3fOKtUw0Xmo=
+dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
+github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
+github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
 github.com/Microsoft/go-winio v0.5.2 h1:a9IhgEQBCUEk6QCdml9CiJGhAws+YwffDHEMp1VMrpA=
 github.com/Microsoft/go-winio v0.5.2/go.mod h1:WpS1mjBmmwHBEWmogvA2mj8546UReBk4v8QkMxJ6pZY=
 github.com/ProtonMail/go-crypto v0.0.0-20230217124315-7d5c6f04bbb8 h1:wPbRQzjjwFc0ih8puEVAOFGELsn1zoIIYdxvML7mDxA=
@@ -10,14 +50,32 @@ github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5 h1:0CwZNZbxp69SHPd
 github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5/go.mod h1:wHh0iHkYZB8zMSxRWpUBQtwG5a7fFgvEO+odwuTv2gs=
 github.com/benbjohnson/clock v1.1.0 h1:Q92kusRqC1XV2MjkWETPvjJVqKetz1OzxZB7mHJLju8=
 github.com/bwesterb/go-ristretto v1.2.0/go.mod h1:fUIoIZaG73pV5biE2Blr2xEzDoMj7NFEuV9ekS419A0=
+github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU=
+github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI=
+github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI=
+github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU=
+github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw=
 github.com/cloudflare/circl v1.1.0 h1:bZgT/A+cikZnKIwn7xL2OBj012Bmvho/o6RpRvv3GKY=
 github.com/cloudflare/circl v1.1.0/go.mod h1:prBCrKB9DV4poKZY1l9zBXg2QJY7mvgRvtMxxK7fi4I=
+github.com/cncf/udpa/go v0.0.0-20191209042840-269d4d468f6f/go.mod h1:M8M6+tZqaGXZJjfX53e64911xZQV5JYwmTeXPW+k8Sc=
+github.com/cncf/udpa/go v0.0.0-20200629203442-efcf912fb354/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
+github.com/cncf/udpa/go v0.0.0-20201120205902-5459f2c99403/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk=
+github.com/cpuguy83/go-md2man/v2 v2.0.2/go.mod h1:tgQtvFlXSQOSOSIRvRPT7W67SCa46tRHOmNcaadrF8o=
 github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/emirpasic/gods v1.18.1 h1:FXtiHYKDGKCW2KzwZKx0iC0PQmdlorYgdFG9jPXJ1Bc=
 github.com/emirpasic/gods v1.18.1/go.mod h1:8tpGGwCnJ5H4r6BWwaV6OrWmMoPhUl5jm/FMNAnJvWQ=
+github.com/envoyproxy/go-control-plane v0.9.0/go.mod h1:YTl/9mNaCwkRvm6d1a2C3ymFceY/DCBVvsKhRF0iEA4=
+github.com/envoyproxy/go-control-plane v0.9.1-0.20191026205805-5f8ba28d4473/go.mod h1:YTl/9mNaCwkRvm6d1a2C3ymFceY/DCBVvsKhRF0iEA4=
+github.com/envoyproxy/go-control-plane v0.9.4/go.mod h1:6rpuAdCZL397s3pYoYcLgu1mIlRU8Am5FuJP05cCM98=
+github.com/envoyproxy/go-control-plane v0.9.7/go.mod h1:cwu0lG7PUMfa9snN8LXBig5ynNVH9qI8YYLbd1fK2po=
+github.com/envoyproxy/go-control-plane v0.9.9-0.20201210154907-fd9021fe5dad/go.mod h1:cXg6YxExXjJnVBQHBLXeUAgxn2UodCpnH306RInaBQk=
+github.com/envoyproxy/protoc-gen-validate v0.1.0/go.mod h1:iSmxcyjqTsJpI2R4NaDN7+kN2VEUnK/pcBlmesArF7c=
+github.com/frankban/quicktest v1.14.3 h1:FJKSZTDHjyhriyC81FLQ0LY93eSai0ZyR/ZIkd3ZUKE=
+github.com/fsnotify/fsnotify v1.6.0 h1:n+5WquG0fcWoWp6xPWfHdbskMCQaFnG6PfBrh1Ky4HY=
+github.com/fsnotify/fsnotify v1.6.0/go.mod h1:sl3t1tCWJFWoRz9R8WJCbQihKKwmorjAbSClcnxKAGw=
 github.com/gliderlabs/ssh v0.3.5 h1:OcaySEmAQJgyYcArR+gGGTHCyE7nvhEMTlYY+Dp8CpY=
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@@ -29,11 +87,48 @@ github.com/go-git/go-git-fixtures/v4 v4.3.1 h1:y5z6dd3qi8Hl+stezc8p3JxDkoTRqMAlK
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@@ -126,6 +408,7 @@ golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8/go.mod h1:oPkhp1MJrh7nUepCBc
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@@ -137,36 +420,193 @@ golang.org/x/term v0.0.0-20220722155259-a9ba230a4035/go.mod h1:jbD1KX2456YbFQfuX
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 google.golang.org/protobuf v1.26.0/go.mod h1:9q0QmTI4eRPtz6boOQmLYwt+qCgq0jsYwAQnmE0givc=
-google.golang.org/protobuf v1.28.0 h1:w43yiav+6bVFTBQFZX0r7ipe9JQ1QsbMgHwbBziscLw=
-google.golang.org/protobuf v1.28.0/go.mod h1:HV8QOd/L58Z+nl8r43ehVNZIU/HEI6OcFqwMG9pJV4I=
+google.golang.org/protobuf v1.28.1 h1:d0NfwRgPtno5B1Wa6L2DAG+KivqkdutMf1UhdNx175w=
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+honnef.co/go/tools v0.0.1-2020.1.4/go.mod h1:X/FiERA/W4tHapMX5mGpAtMSVEeEUOyHaw9vFzvIQ3k=
+rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8=
 rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4=
+rsc.io/quote/v3 v3.1.0/go.mod h1:yEA65RcK8LyAZtP9Kv3t0HmxON59tX3rD+tICJqUlj0=
+rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA=
diff --git a/llm/code-change-request.tmpl b/llm/code-change-request.tmpl
index 9648bbd..843ed9a 100644
--- a/llm/code-change-request.tmpl
+++ b/llm/code-change-request.tmpl
@@ -17,9 +17,7 @@ Files:
 {{ range $index, $file := .Files }}
   - name: {{ $file.Path }}
     contents:
-    ```
     [new {{ $file.Path }} contents]
-    ```
 {{ end }}
 
 Notes:
diff --git a/llm/common.go b/llm/common.go
index c97f5a7..11a1598 100644
--- a/llm/common.go
+++ b/llm/common.go
@@ -37,7 +37,7 @@ func (req CodeChangeRequest) MustGetPrompt() string {
 
 // GetPrompt converts the information in the request to a prompt for an LLM.
 func (req CodeChangeRequest) GetPrompt() (string, error) {
-	tmpl, err := template.ParseFiles("./code-change-request.tmpl")
+	tmpl, err := template.ParseFiles("./llm/code-change-request.tmpl")
 	if err != nil {
 		return "", err
 	}
diff --git a/main.go b/main.go
new file mode 100644
index 0000000..e9881bd
--- /dev/null
+++ b/main.go
@@ -0,0 +1,7 @@
+package main
+
+import "github.com/mobyvb/pull-pal/cmd"
+
+func main() {
+	cmd.Execute()
+}
diff --git a/pullpal/common.go b/pullpal/common.go
index 9dad586..e5d8d21 100644
--- a/pullpal/common.go
+++ b/pullpal/common.go
@@ -28,7 +28,7 @@ type PullPal struct {
 func NewPullPal(ctx context.Context, log *zap.Logger, self vc.Author, repo vc.Repository) (*PullPal, error) {
 	ghClient, err := vc.NewGithubClient(ctx, log, self, repo)
 	if err != nil {
-		log.Error("Failed to setup Github client.", zap.Error(err))
+		return nil, err
 	}
 
 	return &PullPal{
diff --git a/vc/common.go b/vc/common.go
index 3f1d280..fbcf14f 100644
--- a/vc/common.go
+++ b/vc/common.go
@@ -35,7 +35,7 @@ type Repository struct {
 
 // SSH returns the SSH connection string for the repository.
 func (repo Repository) SSH() string {
-	return fmt.Sprintf("git%s:%s/%s.git", repo.HostDomain, repo.Owner.Handle, repo.Name)
+	return fmt.Sprintf("git@%s:%s/%s.git", repo.HostDomain, repo.Owner.Handle, repo.Name)
 }
 
 // HTTPS returns the HTTPS representation of the remote repository.
@@ -60,6 +60,4 @@ type VCClient interface {
 	ReplaceOrAddLocalFile(newFile llm.File) error
 	// FinishCommit completes a commit, after which a code change request can be opened or updated.
 	FinishCommit(message string) error
-	// Close tears down the VCClient.
-	Close() error
 }
diff --git a/vc/github.go b/vc/github.go
index b47207b..dd03a3b 100644
--- a/vc/github.go
+++ b/vc/github.go
@@ -12,6 +12,7 @@ import (
 	"path/filepath"
 	"strconv"
 	"strings"
+	"time"
 
 	"github.com/mobyvb/pull-pal/llm"
 
@@ -39,7 +40,7 @@ type GithubClient struct {
 
 // NewGithubClient initializes a Github client and checks out a repository locally.
 func NewGithubClient(ctx context.Context, log *zap.Logger, self Author, repo Repository) (*GithubClient, error) {
-	log.Debug("Creating new Github client...")
+	log.Info("Creating new Github client...")
 	if self.Token == "" {
 		return nil, errors.New("Github access token not provided")
 	}
@@ -53,7 +54,16 @@ func NewGithubClient(ctx context.Context, log *zap.Logger, self Author, repo Rep
 	if repo.LocalPath == "" {
 		return nil, errors.New("local path to clone repository not provided")
 	}
-	log.Debug("Cloning repository locally...")
+
+	if repo.LocalPath != "" {
+		// remove local repo if it exists already
+		err := os.RemoveAll(repo.LocalPath)
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	log.Info("Cloning repository locally...", zap.String("local repo path", repo.LocalPath), zap.String("url", repo.SSH()))
 	// TODO this can be done in-memory - see https://pkg.go.dev/github.com/go-git/go-git/v5#readme-in-memory-example
 	localRepo, err := git.PlainClone(repo.LocalPath, false, &git.CloneOptions{
 		URL: repo.SSH(),
@@ -64,12 +74,12 @@ func NewGithubClient(ctx context.Context, log *zap.Logger, self Author, repo Rep
 		},
 	})
 	if err != nil {
-		log.Error("Failed to clone local repo.", zap.Error(err))
+		log.Info("failed")
 		return nil, err
 	}
 	repo.localRepo = localRepo
 
-	log.Debug("Success. Github client set up.")
+	log.Info("Success. Github client set up.")
 
 	return &GithubClient{
 		ctx:    ctx,
@@ -91,10 +101,6 @@ func (gc *GithubClient) OpenCodeChangeRequest(req llm.CodeChangeRequest, res llm
 	remoteName := "origin"
 	body := res.Notes
 	body += fmt.Sprintf("\n\nResolves #%s", req.IssueID)
-	issue, err := strconv.Atoi(req.IssueID)
-	if err != nil {
-		return "", "", err
-	}
 
 	// Create new local branch
 	headRef, err := gc.repo.localRepo.Head()
@@ -139,7 +145,6 @@ func (gc *GithubClient) OpenCodeChangeRequest(req llm.CodeChangeRequest, res llm
 		Head:  &branchName,
 		Base:  &baseBranch,
 		Body:  &body,
-		Issue: &issue,
 	})
 	if err != nil {
 		return "", "", err
@@ -173,7 +178,7 @@ func (gc *GithubClient) ListOpenIssues() ([]Issue, error) {
 		}
 
 		nextIssue := Issue{
-			ID:      strconv.Itoa(int(issue.GetID())),
+			ID:      strconv.Itoa(issue.GetNumber()),
 			Subject: issue.GetTitle(),
 			Body:    issue.GetBody(),
 			URL:     issue.GetHTMLURL(),
@@ -194,6 +199,14 @@ func (gc *GithubClient) GetLocalFile(path string) (llm.File, error) {
 
 	data, err := ioutil.ReadFile(fullPath)
 	if err != nil {
+		// if file doesn't exist, just return an empty file
+		// this means we want to prompt the llm to populate it for the first time
+		if errors.Is(err, os.ErrNotExist) {
+			return llm.File{
+				Path:     path,
+				Contents: "",
+			}, nil
+		}
 		return llm.File{}, err
 	}
 
@@ -255,19 +268,9 @@ func (gc *GithubClient) FinishCommit(message string) error {
 		Author: &object.Signature{
 			Name:  gc.self.Handle,
 			Email: gc.self.Email,
+			When:  time.Now(),
 		},
 	})
 
 	return err
 }
-
-func (gc *GithubClient) Close() error {
-	// Remove local repository
-	if gc.repo.LocalPath != "" {
-		err := os.RemoveAll(gc.repo.LocalPath)
-
-		return err
-	}
-
-	return nil
-}