diff --git a/runtime/lua/man.lua b/runtime/lua/man.lua
index 8a9b01f6d2..5c4a80f9f0 100644
--- a/runtime/lua/man.lua
+++ b/runtime/lua/man.lua
@@ -262,7 +262,7 @@ local function get_path(name, sect)
   -- find any that match the specified name
   --- @param v string
   local namematches = vim.tbl_filter(function(v)
-    local tail = fn.fnamemodify(v, ':t')
+    local tail = vim.fs.basename(v)
     return tail:find(name, 1, true) ~= nil
   end, results) or {}
   local sectmatches = {}
@@ -364,7 +364,7 @@ end
 --- @return string name
 --- @return string sect
 local function parse_path(path)
-  local tail = fn.fnamemodify(path, ':t')
+  local tail = vim.fs.basename(path)
   if
     path:match('%.[glx]z$')
     or path:match('%.bz2$')
diff --git a/runtime/lua/nvim/spellfile.lua b/runtime/lua/nvim/spellfile.lua
index 45bfd5b872..f964d78a2f 100644
--- a/runtime/lua/nvim/spellfile.lua
+++ b/runtime/lua/nvim/spellfile.lua
@@ -119,6 +119,7 @@ local function ensure_target_dir()
     return dirs[1]
   end
 
+  -- vim.fs.relpath does not prepend '~/' while fnamemodify does
   dir = vim.fn.fnamemodify(dir, ':~')
   error(('cannot find a writable spell/ dir in runtimepath, and %s is not usable'):format(dir))
 end
diff --git a/runtime/lua/vim/filetype.lua b/runtime/lua/vim/filetype.lua
index 69374acbbf..f17a3d042d 100644
--- a/runtime/lua/vim/filetype.lua
+++ b/runtime/lua/vim/filetype.lua
@@ -2863,15 +2863,6 @@ local function normalize_path(path, as_pattern)
   return normal
 end
 
-local abspath = function(x)
-  return fn.fnamemodify(x, ':p')
-end
-if fn.has('win32') == 1 then
-  abspath = function(x)
-    return (fn.fnamemodify(x, ':p'):gsub('\\', '/'))
-  end
-end
-
 --- @class vim.filetype.add.filetypes
 --- @inlinedoc
 --- @field pattern? vim.filetype.mapping
@@ -3178,7 +3169,7 @@ function M.match(args)
   if name then
     name = normalize_path(name)
 
-    local path = abspath(name)
+    local path = vim.fs.abspath(name)
     do -- First check for the simple case where the full path exists as a key
       local ft, on_detect = dispatch(filename[path], path, bufnr)
       if ft then
@@ -3186,7 +3177,7 @@ function M.match(args)
       end
     end
 
-    local tail = fn.fnamemodify(name, ':t')
+    local tail = vim.fs.basename(name)
 
     do -- Next check against just the file name
       local ft, on_detect = dispatch(filename[tail], path, bufnr)
diff --git a/runtime/lua/vim/filetype/detect.lua b/runtime/lua/vim/filetype/detect.lua
index dfb3cee20c..0ac39ba155 100644
--- a/runtime/lua/vim/filetype/detect.lua
+++ b/runtime/lua/vim/filetype/detect.lua
@@ -18,6 +18,7 @@
 --     `if line =~ '^\s*unwind_protect\>'` => `if matchregex(line, [[\c^\s*unwind_protect\>]])`
 
 local fn = vim.fn
+local fs = vim.fs
 
 local M = {}
 
@@ -395,7 +396,7 @@ end
 
 --- @type vim.filetype.mapfn
 function M.dat(path, bufnr)
-  local file_name = fn.fnamemodify(path, ':t'):lower()
+  local file_name = fs.basename(path):lower()
   -- Innovation data processing
   if findany(file_name, { '^upstream%.dat$', '^upstream%..*%.dat$', '^.*%.upstream%.dat$' }) then
     return 'upstreamdat'
@@ -423,7 +424,7 @@ end
 -- to non-dep3patch files, such as README and other text files.
 --- @type vim.filetype.mapfn
 function M.dep3patch(path, bufnr)
-  local file_name = fn.fnamemodify(path, ':t')
+  local file_name = fs.basename(path)
   if file_name == 'series' then
     return
   end
@@ -562,7 +563,7 @@ function M.dsp(path, bufnr)
   end
 
   -- Test the filename
-  local file_name = fn.fnamemodify(path, ':t')
+  local file_name = fs.basename(path)
   if file_name:find('^[mM]akefile.*$') then
     return 'make'
   end
@@ -773,7 +774,7 @@ end
 --- @return boolean
 local function is_hare_module(dir, depth)
   depth = math.max(depth, 0)
-  for name, _ in vim.fs.dir(dir, { depth = depth + 1 }) do
+  for name, _ in fs.dir(dir, { depth = depth + 1 }) do
     if name:find('%.ha$') then
       return true
     end
@@ -784,7 +785,7 @@ end
 --- @type vim.filetype.mapfn
 function M.haredoc(path, _)
   if vim.g.filetype_haredoc then
-    if is_hare_module(vim.fs.dirname(path), vim.g.haredoc_search_depth or 1) then
+    if is_hare_module(fs.dirname(path), vim.g.haredoc_search_depth or 1) then
       return 'haredoc'
     end
   end
@@ -1064,8 +1065,8 @@ end
 ---  – files in POSIX M4
 --- @type vim.filetype.mapfn
 function M.m4(path, bufnr)
-  local fname = fn.fnamemodify(path, ':t')
-  path = fn.fnamemodify(path, ':p:h')
+  local fname = fs.basename(path)
+  path = fs.dirname(fs.abspath(path))
 
   if fname:find('html%.m4$') then
     return 'htmlm4'
@@ -1121,7 +1122,7 @@ function M.make(path, bufnr)
   vim.b.make_flavor = nil
 
   -- 1. filename
-  local file_name = fn.fnamemodify(path, ':t')
+  local file_name = fs.basename(path)
   if file_name == 'BSDmakefile' then
     vim.b.make_flavor = 'bsd'
     return 'make'
@@ -1187,7 +1188,7 @@ end
 --- @param path string
 --- @return string?
 function M.me(path)
-  local filename = fn.fnamemodify(path, ':t'):lower()
+  local filename = fs.basename(path):lower()
   if filename ~= 'read.me' and filename ~= 'click.me' then
     return 'nroff'
   end
@@ -1297,7 +1298,7 @@ end
 --- (Slow test) If a file contains a 'use' statement then it is almost certainly a Perl file.
 --- @type vim.filetype.mapfn
 function M.perl(path, bufnr)
-  local dir_name = vim.fs.dirname(path)
+  local dir_name = fs.dirname(path)
   if fn.fnamemodify(path, '%:e') == 't' and (dir_name == 't' or dir_name == 'xt') then
     return 'perl'
   end
@@ -1529,7 +1530,7 @@ function M.rules(path)
       return 'hog'
     end
     --- @cast config_lines -string
-    local dir = fn.fnamemodify(path, ':h')
+    local dir = fs.dirname(path)
     for _, line in ipairs(config_lines) do
       local match = line:match(udev_rules_pattern)
       if match then
diff --git a/runtime/lua/vim/health/health.lua b/runtime/lua/vim/health/health.lua
index 090f0b3d30..6dafceeae3 100644
--- a/runtime/lua/vim/health/health.lua
+++ b/runtime/lua/vim/health/health.lua
@@ -215,7 +215,7 @@ local function check_rplugin_manifest()
       local contents = vim.fn.join(vim.fn.readfile(script))
       if vim.regex([[\<\%(from\|import\)\s\+neovim\>]]):match_str(contents) then
         if vim.regex([[[\/]__init__\.py$]]):match_str(script) then
-          script = vim.fn.tr(vim.fn.fnamemodify(script, ':h'), '\\', '/')
+          script = vim.fs.normalize(vim.fs.dirname(script))
         end
         if not existing_rplugins[script] then
           local msg = vim.fn.printf('"%s" is not registered.', vim.fs.basename(path))
diff --git a/runtime/lua/vim/loader.lua b/runtime/lua/vim/loader.lua
index 187d7076de..c5279990d1 100644
--- a/runtime/lua/vim/loader.lua
+++ b/runtime/lua/vim/loader.lua
@@ -429,7 +429,7 @@ function M.enable(enable)
   M.enabled = enable
 
   if enable then
-    vim.fn.mkdir(vim.fn.fnamemodify(M.path, ':p'), 'p')
+    vim.fn.mkdir(vim.fs.abspath(M.path), 'p')
     _G.loadfile = loadfile_cached
     -- add Lua loader
     table.insert(loaders, 2, loader_cached)
diff --git a/runtime/lua/vim/lsp/health.lua b/runtime/lua/vim/lsp/health.lua
index d84e27d13a..14502851a5 100644
--- a/runtime/lua/vim/lsp/health.lua
+++ b/runtime/lua/vim/lsp/health.lua
@@ -91,6 +91,7 @@ local function check_active_clients()
       else
         dirs_info = string.format(
           '- Root directory: %s',
+          -- vim.fs.relpath does not prepend '~/' while fnamemodify does
           client.root_dir and vim.fn.fnamemodify(client.root_dir, ':~')
         ) or nil
       end
diff --git a/runtime/lua/vim/provider/health.lua b/runtime/lua/vim/provider/health.lua
index cfd2d2f9bc..bdf67212b0 100644
--- a/runtime/lua/vim/provider/health.lua
+++ b/runtime/lua/vim/provider/health.lua
@@ -535,18 +535,12 @@ local function version_info(python)
     return { python_version, 'unable to load neovim Python module', pypi_version, nvim_path }
   end
 
-  -- Assuming that multiple versions of a package are installed, sort them
-  -- numerically in descending order.
+  -- Assuming that multiple versions of a package are installed as
+  -- `<semver>/<metapath>`, sort them on semantic version in descending order.
   local function compare(metapath1, metapath2)
-    local a = vim.fn.matchstr(vim.fn.fnamemodify(metapath1, ':p:h:t'), [[[0-9.]\+]])
-    local b = vim.fn.matchstr(vim.fn.fnamemodify(metapath2, ':p:h:t'), [[[0-9.]\+]])
-    if a == b then
-      return 0
-    elseif a > b then
-      return 1
-    else
-      return -1
-    end
+    local dir1 = vim.fs.basename(vim.fs.dirname(vim.fs.abspath(metapath1)))
+    local dir2 = vim.fs.basename(vim.fs.dirname(vim.fs.abspath(metapath2)))
+    return vim.version.cmp(dir1, dir2)
   end
 
   -- Try to get neovim.VERSION (added in 0.1.11dev).
@@ -576,6 +570,7 @@ local function version_info(python)
     end
   end
 
+  -- vim.fs.relpath does not prepend '~/' while fnamemodify does
   local nvim_path_base = vim.fn.fnamemodify(nvim_path, [[:~:h]])
   local version_status = 'unknown; ' .. nvim_path_base
   if not is_bad_response(nvim_version) and not is_bad_response(pypi_version) then
diff --git a/runtime/lua/vim/treesitter/_query_linter.lua b/runtime/lua/vim/treesitter/_query_linter.lua
index 8cab984598..7bfc860111 100644
--- a/runtime/lua/vim/treesitter/_query_linter.lua
+++ b/runtime/lua/vim/treesitter/_query_linter.lua
@@ -40,8 +40,9 @@ end
 local function guess_query_lang(buf)
   local filename = api.nvim_buf_get_name(buf)
   if filename ~= '' then
-    local resolved_filename = vim.F.npcall(vim.fn.fnamemodify, filename, ':p:h:t')
-    return resolved_filename and vim.treesitter.language.get_lang(resolved_filename)
+    -- get <lang> from /path/<lang>/<query_type>.scm
+    local resolved = vim.fs.basename(vim.fs.dirname(vim.fs.abspath(filename)))
+    return vim.treesitter.language.get_lang(resolved)
   end
 end
 
diff --git a/runtime/lua/vim/treesitter/dev.lua b/runtime/lua/vim/treesitter/dev.lua
index 589dc00fe1..246525757d 100644
--- a/runtime/lua/vim/treesitter/dev.lua
+++ b/runtime/lua/vim/treesitter/dev.lua
@@ -378,7 +378,7 @@ function M.inspect_tree(opts)
   local opts_title = opts.title
   if not opts_title then
     local bufname = api.nvim_buf_get_name(buf)
-    title = string.format('Syntax tree for %s', vim.fn.fnamemodify(bufname, ':.'))
+    title = ('Syntax tree for %s'):format(vim.fs.relpath('.', bufname))
   elseif type(opts_title) == 'function' then
     title = opts_title(buf)
   end
diff --git a/runtime/lua/vim/treesitter/health.lua b/runtime/lua/vim/treesitter/health.lua
index 28571fa9a3..881d6e46a6 100644
--- a/runtime/lua/vim/treesitter/health.lua
+++ b/runtime/lua/vim/treesitter/health.lua
@@ -101,7 +101,7 @@ function M.check()
       end)
 
       for _, query in ipairs(queries) do
-        local dir = vim.fn.fnamemodify(query.path, ':h')
+        local dir = vim.fs.dirname(query.path)
         health.ok(string.format('%-15s %-15s %s', lang, query.type, dir))
       end
     end