diff --git a/main.go b/main.go
index d5dfd44..d134eba 100644
--- a/main.go
+++ b/main.go
@@ -2,22 +2,16 @@ package main
 
 import (
 	"flag"
-	"github.com/BurntSushi/toml"
-	wikilink "github.com/abhinav/goldmark-wikilink"
-	"github.com/yuin/goldmark"
 	"io/ioutil"
 	"path/filepath"
 	"time"
+
+	"github.com/BurntSushi/toml"
+	"github.com/yuin/goldmark"
 )
 
 var md goldmark.Markdown
 
-func init() {
-	md = goldmark.New(
-		goldmark.WithExtensions(&wikilink.Extender{}),
-	)
-}
-
 type Link struct {
 	Source string `json:"source"`
 	Target string `json:"target"`
diff --git a/parse.go b/parse.go
index a36c71d..cf0e65b 100644
--- a/parse.go
+++ b/parse.go
@@ -3,13 +3,15 @@ package main
 import (
 	"bytes"
 	"fmt"
-	"github.com/PuerkitoBio/goquery"
 	"io/ioutil"
 	"strings"
+
+	"github.com/PuerkitoBio/goquery"
+	"github.com/yuin/goldmark"
 )
 
 // parse single file for links
-func parse(dir, pathPrefix string) []Link {
+func parse(md goldmark.Markdown, fileIndex fileIndex, dir, pathPrefix string) []Link {
 	// read file
 	source, err := ioutil.ReadFile(dir)
 	if err != nil {
@@ -37,8 +39,10 @@ func parse(dir, pathPrefix string) []Link {
 		target = processTarget(target)
 		source := processSource(trim(dir, pathPrefix, ".md"))
 
+		target = fileIndex.resolve(target)
+
 		// fmt.Printf("  '%s' => %s\n", source, target)
-		if !strings.HasPrefix(text, "^"){
+		if !strings.HasPrefix(text, "^") {
 			links = append(links, Link{
 				Source: source,
 				Target: target,
diff --git a/walk.go b/walk.go
index 34e3795..978d130 100644
--- a/walk.go
+++ b/walk.go
@@ -9,7 +9,9 @@ import (
 	"strings"
 	"time"
 
+	wikilink "github.com/abhinav/goldmark-wikilink"
 	"github.com/adrg/frontmatter"
+	"github.com/yuin/goldmark"
 	"gopkg.in/yaml.v2"
 )
 
@@ -19,6 +21,60 @@ type Front struct {
 	Tags  []string `yaml:"tags"`
 }
 
+type fileIndex struct {
+	index map[string]string
+}
+
+// resolve takes a link path and attempts to canonicalize it according to this
+// fileIndex. If a matching canonical link cannot be found, the link is returned
+// untouched.
+func (i *fileIndex) resolve(path string) string {
+	if !isInternal(path) {
+		return path
+	}
+
+	trimmedPath := strings.TrimLeft(path, "/")
+
+	// If the path has any degree of nesting built into it, treat it as an absolute path
+	if strings.Contains(trimmedPath, "/") {
+		return path
+	}
+
+	resolved, ok := i.index[trimmedPath]
+	if ok {
+		target := processTarget(resolved)
+		return target
+	}
+
+	return path
+}
+
+func buildFileIndex(root, ext string, ignorePaths map[string]struct{}) (fileIndex, error) {
+	index := map[string]string{}
+	err := filepath.WalkDir(root, func(fp string, d fs.DirEntry, e error) error {
+		if e != nil {
+			return e
+		}
+
+		// path normalize fp
+		s := filepath.ToSlash(fp)
+		s = strings.ReplaceAll(s, " ", "-")
+		if _, ignored := ignorePaths[s]; ignored {
+			return nil
+		} else if filepath.Ext(d.Name()) == ext {
+			base := filepath.Base(strings.TrimSuffix(s, ".md"))
+			index[base] = strings.TrimPrefix(s, root)
+		}
+
+		return nil
+	})
+	if err != nil {
+		return fileIndex{}, err
+	}
+
+	return fileIndex{index: index}, nil
+}
+
 // recursively walk directory and return all files with given extension
 func walk(root, ext string, index bool, ignorePaths map[string]struct{}) (res []Link, i ContentIndex) {
 	fmt.Printf("Scraping %s\n", root)
@@ -32,7 +88,15 @@ func walk(root, ext string, index bool, ignorePaths map[string]struct{}) (res []
 
 	start := time.Now()
 
-	err := filepath.WalkDir(root, func(fp string, d fs.DirEntry, e error) error {
+	md := goldmark.New(
+		goldmark.WithExtensions(&wikilink.Extender{}))
+
+	fileIndex, err := buildFileIndex(root, ext, ignorePaths)
+	if err != nil {
+		panic(err)
+	}
+
+	err = filepath.WalkDir(root, func(fp string, d fs.DirEntry, e error) error {
 		if e != nil {
 			return e
 		}
@@ -69,10 +133,10 @@ func walk(root, ext string, index bool, ignorePaths map[string]struct{}) (res []
 						title = strings.TrimSuffix(filepath.Base(fileName), filepath.Ext(fileName))
 					}
 
-          // default tags
-          if matter.Tags == nil {
-            matter.Tags = []string{}
-          }
+					// default tags
+					if matter.Tags == nil {
+						matter.Tags = []string{}
+					}
 
 					// add to content and link index
 					i[source] = Content{
@@ -81,7 +145,7 @@ func walk(root, ext string, index bool, ignorePaths map[string]struct{}) (res []
 						Content:      body,
 						Tags:         matter.Tags,
 					}
-					res = append(res, parse(s, root)...)
+					res = append(res, parse(md, fileIndex, s, root)...)
 				} else {
 					fmt.Printf("[Ignored] %s\n", d.Name())
 					nPrivate++