diff --git a/tools/list_files.js b/tools/list_files.js
index ec3f699..8e6ef1b 100644
--- a/tools/list_files.js
+++ b/tools/list_files.js
@@ -132,9 +132,10 @@ export async function run(args) {
   let chrootResolved;
   try {
     chrootResolved = path.resolve(chrootPath);
-    await fs.access(chrootResolved); // Ensure chroot path exists
+    // Auto-create the chroot base directory if it does not exist
+    await fs.mkdir(chrootResolved, { recursive: true });
   } catch (err) {
-    return { err: `Invalid chroot path: ${chrootPath} (${err?.message || String(err)})` };
+    return { err: `Failed to prepare chroot path: ${chrootPath} (${err?.message || String(err)})` };
   }
 
   let resolvedBase;
diff --git a/tools/patch_files.js b/tools/patch_files.js
index cfa0864..2b4d36f 100644
--- a/tools/patch_files.js
+++ b/tools/patch_files.js
@@ -102,39 +102,53 @@ class Patch {
 // --------------------------------------------------------------------------- //
 //  Path utilities for chroot functionality
 // --------------------------------------------------------------------------- //
-function normalizePath(path) {
-    return path.replace(/\\/g, '/').replace(/\/+/g, '/');
+function normalizePath(p) {
+    return (p || '').replace(/\\/g, '/').replace(/\/+/g, '/');
 }
 
-function joinPaths(...paths) {
-    return normalizePath(paths.filter(p => p).join('/'));
+function joinPaths(...parts) {
+    const joined = parts.filter(Boolean).join('/');
+    return normalizePath(joined);
 }
 
 function resolvePath(chroot, filepath) {
-    if (!chroot) return filepath;
+    const file = normalizePath(filepath);
+    if (!chroot) return file;
     
-    // Remove leading slash from filepath if present
-    const cleanFilepath = filepath.startsWith('/') ? filepath.substring(1) : filepath;
+    const root = normalizePath(chroot);
     
-    // Join chroot and filepath
-    const resolved = joinPaths(chroot, cleanFilepath);
+    // If file is absolute, treat it as relative to chroot
+    if (file.startsWith('/')) {
+        // Remove leading slash and join with chroot
+        const relativePath = file.substring(1);
+        const resolved = joinPaths(root, relativePath);
+        return resolved.startsWith('/') ? resolved : '/' + resolved;
+    }
     
-    // Ensure it starts with /
+    // If file is relative, join with chroot
+    const resolved = joinPaths(root, file);
     return resolved.startsWith('/') ? resolved : '/' + resolved;
 }
 
 function unresolvePath(chroot, filepath) {
-    if (!chroot) return filepath;
+    const file = normalizePath(filepath);
+    if (!chroot) return file;
     
-    const chrootPath = chroot.startsWith('/') ? chroot : '/' + chroot;
-    const cleanFilepath = filepath.startsWith('/') ? filepath : '/' + filepath;
+    const root = normalizePath(chroot);
+    const rootWithSlash = root.endsWith('/') ? root : root + '/';
     
-    if (cleanFilepath.startsWith(chrootPath)) {
-        const relativePath = cleanFilepath.substring(chrootPath.length);
-        return relativePath.startsWith('/') ? relativePath : '/' + relativePath;
+    // Convert absolute path back to what user would expect
+    if (file.startsWith(rootWithSlash)) {
+        // Return path relative to chroot (without leading slash for user expectation)
+        return file.substring(rootWithSlash.length);
     }
     
-    return filepath;
+    if (file === root) {
+        return '';
+    }
+    
+    // If somehow outside chroot, return as-is
+    return file;
 }
 
 // --------------------------------------------------------------------------- //
@@ -409,6 +423,11 @@ function find_context_core(lines, context, start) {
 }
 
 function find_context(lines, context, start, eof) {
+    // Special case: if context is empty, return start position
+    if (!context || context.length === 0) {
+        return [start, 0];
+    }
+    
     if (eof) {
         let [new_index, fuzz] = find_context_core(lines, context, Math.max(0, lines.length - context.length));
         if (new_index !== -1) {
@@ -461,16 +480,20 @@ function peek_next_section(lines, index) {
         }
         s = s.substring(1);
 
-        if (mode === "keep" && last_mode !== mode) {
-            if (ins_lines.length > 0 || del_lines.length > 0) {
-                chunks.push(
-                    new Chunk(
-                        old.length - del_lines.length,
-                        [...del_lines],
-                        [...ins_lines]
-                    )
-                );
-            }
+        // Handle the case where we're at the beginning and have content
+        if (index === orig_index + 1 && old.length === 0 && (del_lines.length > 0 || ins_lines.length > 0)) {
+            // This is the first content line, start collecting
+        }
+
+        if (mode === "keep" && last_mode !== mode && (ins_lines.length > 0 || del_lines.length > 0)) {
+            const chunk_orig_index = old.length - del_lines.length;
+            chunks.push(
+                new Chunk(
+                    chunk_orig_index,
+                    [...del_lines],
+                    [...ins_lines]
+                )
+            );
             del_lines = [];
             ins_lines = [];
         }
@@ -485,10 +508,12 @@ function peek_next_section(lines, index) {
         }
     }
 
+    // Handle any remaining content
     if (ins_lines.length > 0 || del_lines.length > 0) {
+        const chunk_orig_index = old.length - del_lines.length;
         chunks.push(
             new Chunk(
-                old.length - del_lines.length,
+                chunk_orig_index,
                 [...del_lines],
                 [...ins_lines]
             )
@@ -654,8 +679,16 @@ function identify_files_added(text, chroot = null) {
 // --------------------------------------------------------------------------- //
 function load_files(paths, open_fn) {
     const result = {};
-    for (const path of paths) {
-        result[path] = open_fn(path);
+    for (const p of paths) {
+        try {
+            result[p] = open_fn(p);
+        } catch (err) {
+            // Skip truly missing files so parser can emit precise DiffErrors
+            if (err && (err.code === 'ENOENT' || /ENOENT/.test(String(err)))) {
+                continue;
+            }
+            throw err;
+        }
     }
     return result;
 }
@@ -686,7 +719,12 @@ function process_patch(text, open_fn, write_fn, remove_fn, chroot = null) {
     if (!text.startsWith("*** Begin Patch")) {
         throw new DiffError("Patch text must start with *** Begin Patch");
     }
-    const paths = identify_files_needed(text, chroot);
+    // Load update/delete targets and also attempt to load add targets
+    // so existing files are detected during parsing
+    const paths = [
+        ...identify_files_needed(text, chroot),
+        ...identify_files_added(text, chroot),
+    ];
     const orig = load_files(paths, open_fn);
     const [patch, _fuzz] = text_to_patch(text, orig, chroot);
     const commit = patch_to_commit(patch, orig, chroot);
@@ -755,4 +793,4 @@ export async function run(args) {
         }
         throw error;
     }
-}
+}
\ No newline at end of file