diff --git a/DocGen4/Output.lean b/DocGen4/Output.lean
index 4412ec5..5483cfe 100644
--- a/DocGen4/Output.lean
+++ b/DocGen4/Output.lean
@@ -80,8 +80,8 @@ def sourceLinker (ws : Lake.Workspace) (leanHash : String): IO (Name → Option
     | some range => s!"{basic}#L{range.pos.line}-L{range.endPos.line}"
     | none => basic
 
-def htmlOutput (result : AnalyzerResult) (root : String) (ws : Lake.Workspace) (leanHash: String) : IO Unit := do
-  let config := { root := root, result := result, currentName := none, sourceLinker := ←sourceLinker ws leanHash}
+def htmlOutput (result : AnalyzerResult) (ws : Lake.Workspace) (leanHash: String) : IO Unit := do
+  let config : SiteContext := { depthToRoot := 0, result := result, currentName := none, sourceLinker := ←sourceLinker ws leanHash}
   let basePath := FilePath.mk "." / "build" / "doc"
   let indexHtml := ReaderT.run index config 
   let findHtml := ReaderT.run find config
@@ -94,8 +94,10 @@ def htmlOutput (result : AnalyzerResult) (root : String) (ws : Lake.Workspace) (
   for (_, mod) in result.moduleInfo.toArray do
     for decl in filterMapDocInfo mod.members do
       let name := decl.getName.toString
+      let config := { config with depthToRoot := 2 }
       let doc := decl.getDocString.getD ""
-      let link := root ++ s!"semantic/{decl.getName.hash}.xml#"
+      let root := Id.run <| ReaderT.run (getRoot) config
+      let link :=  root ++ s!"../semantic/{decl.getName.hash}.xml#"
       let docLink := Id.run <| ReaderT.run (declNameToLink decl.getName) config
       let sourceLink := Id.run <| ReaderT.run (getSourceUrl mod.name decl.getDeclarationRange) config
       let obj := Json.mkObj [("name", name), ("doc", doc), ("link", link), ("docLink", docLink), ("sourceLink", sourceLink)]
@@ -116,7 +118,8 @@ def htmlOutput (result : AnalyzerResult) (root : String) (ws : Lake.Workspace) (
   FS.writeFile declarationDataPath json.compress
   FS.writeFile (basePath / "declaration-data.timestamp") <| toString (←declarationDataPath.metadata).modified.sec
 
-  FS.writeFile (basePath / "site-root.js") (siteRootJs.replace "{siteRoot}" config.root) 
+  let root := Id.run <| ReaderT.run (getRoot) config
+  FS.writeFile (basePath / "site-root.js") (siteRootJs.replace "{siteRoot}" root) 
   FS.writeFile (basePath / "declaration-data.js") declarationDataCenterJs
   FS.writeFile (basePath / "nav.js") navJs
   FS.writeFile (basePath / "find" / "find.js") findJs
@@ -125,10 +128,14 @@ def htmlOutput (result : AnalyzerResult) (root : String) (ws : Lake.Workspace) (
   FS.writeFile (basePath / "mathjax-config.js") mathjaxConfigJs
 
   for (module, content) in result.moduleInfo.toArray do
+    let fileDir := moduleNameToDirectory basePath module
+    let filePath := moduleNameToFile basePath module
+    -- path: 'basePath/module/components/till/last.html'
+    -- The last component is the file name, so we drop it from the depth to root.
+    let config := { config with depthToRoot := module.components.dropLast.length }
     let moduleHtml := ReaderT.run (moduleToHtml content) config
-    let path := moduleNameToFile basePath module
-    FS.createDirAll $ moduleNameToDirectory basePath module
-    FS.writeFile path moduleHtml.toString
+    FS.createDirAll $ fileDir
+    FS.writeFile filePath moduleHtml.toString
 
 end DocGen4
 
diff --git a/DocGen4/Output/Base.lean b/DocGen4/Output/Base.lean
index 2f84500..2bae54a 100644
--- a/DocGen4/Output/Base.lean
+++ b/DocGen4/Output/Base.lean
@@ -14,10 +14,9 @@ open scoped DocGen4.Jsx
 open Lean System Widget Elab
 
 structure SiteContext where
-  root : String
   result : AnalyzerResult
+  depthToRoot: Nat
   currentName : Option Name
-  -- Generates a URL pointing to the source of the given module Name
   sourceLinker : Name → Option DeclarationRange → String
 
 def setCurrentName (name : Name) (ctx : SiteContext) := {ctx with currentName := some name}
@@ -25,7 +24,13 @@ def setCurrentName (name : Name) (ctx : SiteContext) := {ctx with currentName :=
 abbrev HtmlT := ReaderT SiteContext
 abbrev HtmlM := HtmlT Id
 
-def getRoot : HtmlM String := do pure (←read).root
+def getRoot : HtmlM String := do
+  let rec go: Nat -> String
+  | 0 => "./"
+  | Nat.succ n' => "../" ++ go n'
+  let d <- SiteContext.depthToRoot <$> read
+  return (go d)
+
 def getResult : HtmlM AnalyzerResult := do pure (←read).result
 def getCurrentName : HtmlM (Option Name) := do pure (←read).currentName
 def getSourceUrl (module : Name) (range : Option DeclarationRange): HtmlM String := do pure $ (←read).sourceLinker module range
@@ -35,7 +40,7 @@ def templateExtends {α β : Type} (base : α → HtmlM β) (new : HtmlM α) : H
 
 def moduleNameToLink (n : Name) : HtmlM String := do
   let parts := n.components.map Name.toString
-  pure $ (←getRoot) ++ (parts.intersperse "/").foldl (· ++ ·) "" ++ ".html"
+  pure $ (← getRoot) ++ (parts.intersperse "/").foldl (· ++ ·) "" ++ ".html"
 
 def moduleNameToFile (basePath : FilePath) (n : Name) : FilePath :=
   let parts := n.components.map Name.toString
diff --git a/Main.lean b/Main.lean
index e8b2d82..8bb1187 100644
--- a/Main.lean
+++ b/Main.lean
@@ -5,7 +5,6 @@ import Cli
 open DocGen4 Lean Cli
 
 def runDocGenCmd (p : Parsed) : IO UInt32 := do
-  let root := p.positionalArg! "root" |>.as! String
   let modules : List String := p.variableArgsAs! String |>.toList
   let res ← lakeSetup modules
   match res with
@@ -13,7 +12,7 @@ def runDocGenCmd (p : Parsed) : IO UInt32 := do
     IO.println s!"Loading modules from: {←searchPathRef.get}"
     let doc ← load $ modules.map Name.mkSimple
     IO.println "Outputting HTML"
-    htmlOutput doc root ws leanHash
+    htmlOutput doc ws leanHash
     pure 0
   | Except.error rc => pure rc
 
@@ -22,7 +21,6 @@ def docGenCmd : Cmd := `[Cli|
   "A documentation generator for Lean 4."
 
   ARGS:
-    root : String; "The root URL to generate the HTML for (will be relative in the future)"
     ...modules : String; "The modules to generate the HTML for"
 ]
 
diff --git a/README.md b/README.md
index 7c343a5..7e1f829 100644
--- a/README.md
+++ b/README.md
@@ -4,10 +4,10 @@ Document Generator for Lean 4
 ## Usage
 You can call `doc-gen4` from the top of a Lake project like this:
 ```sh
-$ /path/to/doc-gen4 / Module
+$ /path/to/doc-gen4 Module
 ```
-Where the `/` is the root URL the HTML will refer to and `Module` is one or
-more of the top level modules you want to document.
+
+where `Module` is one or more of the top level modules you want to document.
 The tool will then proceed to compile the project using lake (if that hasn't happened yet),
 analyze it and put the result in `./build/doc`.
 You could e.g. host the files locally with the built-in Python webserver:
diff --git a/deploy_docs.sh b/deploy_docs.sh
index 2f77858..d9d89bc 100755
--- a/deploy_docs.sh
+++ b/deploy_docs.sh
@@ -23,7 +23,7 @@ fi
 
 # generate the docs
 cd $1
-../$2/build/bin/doc-gen4 /mathlib4_docs/ Mathlib
+../$2/build/bin/doc-gen4 Mathlib
 
 if [ "$3" = "true" ]; then
   cd ..