diff --git a/src/compiler/glsl/gl_nir_linker.c b/src/compiler/glsl/gl_nir_linker.c
index 8f6d4ee39b9..de1a7927680 100644
--- a/src/compiler/glsl/gl_nir_linker.c
+++ b/src/compiler/glsl/gl_nir_linker.c
@@ -781,8 +781,15 @@ check_image_resources(const struct gl_constants *consts,
 bool
 gl_nir_link_glsl(const struct gl_constants *consts,
                  const struct gl_extensions *exts,
+                 gl_api api,
                  struct gl_shader_program *prog)
 {
+   if (prog->NumShaders == 0)
+      return true;
+
+   if (!gl_nir_link_varyings(consts, exts, api, prog))
+      return false;
+
    for (unsigned i = 0; i < MESA_SHADER_STAGES; i++) {
       struct gl_linked_shader *shader = prog->_LinkedShaders[i];
       if (shader) {
diff --git a/src/compiler/glsl/gl_nir_linker.h b/src/compiler/glsl/gl_nir_linker.h
index df5d9fb8ba2..b07b18d45d7 100644
--- a/src/compiler/glsl/gl_nir_linker.h
+++ b/src/compiler/glsl/gl_nir_linker.h
@@ -58,6 +58,7 @@ bool gl_nir_link_spirv(const struct gl_constants *consts,
 
 bool gl_nir_link_glsl(const struct gl_constants *consts,
                       const struct gl_extensions *exts,
+                      gl_api api,
                       struct gl_shader_program *prog);
 
 bool gl_nir_link_uniforms(const struct gl_constants *consts,
diff --git a/src/compiler/glsl/glsl_to_nir.cpp b/src/compiler/glsl/glsl_to_nir.cpp
index 5a920c54a76..601b87fc2ad 100644
--- a/src/compiler/glsl/glsl_to_nir.cpp
+++ b/src/compiler/glsl/glsl_to_nir.cpp
@@ -254,15 +254,6 @@ glsl_to_nir(const struct gl_constants *consts,
    if (shader_prog->Label)
       shader->info.label = ralloc_strdup(shader, shader_prog->Label);
 
-   /* Check for transform feedback varyings specified via the API */
-   shader->info.has_transform_feedback_varyings =
-      shader_prog->TransformFeedback.NumVarying > 0;
-
-   /* Check for transform feedback varyings specified in the Shader */
-   if (shader_prog->last_vert_prog)
-      shader->info.has_transform_feedback_varyings |=
-         shader_prog->last_vert_prog->sh.LinkedTransformFeedback->NumVarying > 0;
-
    if (shader->info.stage == MESA_SHADER_FRAGMENT) {
       shader->info.fs.pixel_center_integer = sh->Program->info.fs.pixel_center_integer;
       shader->info.fs.origin_upper_left = sh->Program->info.fs.origin_upper_left;
diff --git a/src/compiler/glsl/linker.cpp b/src/compiler/glsl/linker.cpp
index 160e3bbf593..f7de2866e27 100644
--- a/src/compiler/glsl/linker.cpp
+++ b/src/compiler/glsl/linker.cpp
@@ -4100,10 +4100,6 @@ link_varyings_and_uniforms(unsigned first, unsigned last,
       break;
    }
 
-   if (!link_varyings(prog, first, last, consts, exts,
-                      api, mem_ctx))
-      return false;
-
    if (!prog->data->LinkStatus)
       return false;
 
diff --git a/src/gallium/drivers/virgl/ci/virpipe-gl-fails.txt b/src/gallium/drivers/virgl/ci/virpipe-gl-fails.txt
index 40ee5c0c868..b3f0eb0726d 100644
--- a/src/gallium/drivers/virgl/ci/virpipe-gl-fails.txt
+++ b/src/gallium/drivers/virgl/ci/virpipe-gl-fails.txt
@@ -536,11 +536,20 @@ spec@arb_shader_texture_lod@execution@arb_shader_texture_lod-texgradcube,Fail
 spec@arb_shader_texture_lod@execution@glsl-fs-shadow2dgradarb-07,Fail
 spec@arb_shader_texture_lod@execution@glsl-fs-shadow2dgradarb-08,Fail
 spec@arb_shader_texture_lod@execution@glsl-fs-shadow2dgradarb-cumulative,Fail
+spec@arb_tessellation_shader@execution@barrier-patch,Fail
 spec@arb_tessellation_shader@execution@double-array-vs-tcs-tes,Fail
 spec@arb_tessellation_shader@execution@double-vs-tcs-tes,Fail
 spec@arb_tessellation_shader@execution@dvec2-vs-tcs-tes,Fail
 spec@arb_tessellation_shader@execution@dvec3-vs-tcs-tes,Fail
 spec@arb_tessellation_shader@execution@gs-primitiveid-instanced,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-float-index-rd-after-barrier,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-float-index-wr-before-barrier,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-vec2-index-rd-after-barrier,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-vec2-index-wr-before-barrier,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-vec3-index-rd-after-barrier,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-vec3-index-wr-before-barrier,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-vec4-index-rd-after-barrier,Fail
+spec@arb_tessellation_shader@execution@variable-indexing@tcs-output-array-vec4-index-wr-before-barrier,Fail
 
 # "	intrinsic copy_deref (ssa_2, ssa_3) (dst_access=0, src_access=0)
 #  error: glsl_get_bare_type(dst->type) == glsl_get_bare_type(src->type) (../src/compiler/nir/nir_validate.c:643)"
diff --git a/src/mesa/state_tracker/st_glsl_to_ir.cpp b/src/mesa/state_tracker/st_glsl_to_ir.cpp
index b1424b0e00f..769226065dc 100644
--- a/src/mesa/state_tracker/st_glsl_to_ir.cpp
+++ b/src/mesa/state_tracker/st_glsl_to_ir.cpp
@@ -139,8 +139,6 @@ link_shader(struct gl_context *ctx, struct gl_shader_program *prog)
       validate_ir_tree(ir);
    }
 
-   build_program_resource_list(&ctx->Const, prog);
-
    ret = st_link_nir(ctx, prog);
 
    return ret;
diff --git a/src/mesa/state_tracker/st_glsl_to_nir.cpp b/src/mesa/state_tracker/st_glsl_to_nir.cpp
index 10df319593d..c379702d94a 100644
--- a/src/mesa/state_tracker/st_glsl_to_nir.cpp
+++ b/src/mesa/state_tracker/st_glsl_to_nir.cpp
@@ -293,6 +293,17 @@ shared_type_info(const struct glsl_type *type, unsigned *size, unsigned *align)
    *align = comp_size * (length == 3 ? 4 : length);
 }
 
+static bool
+st_can_remove_varying_before_linking(nir_variable *var, void *data)
+{
+   bool *is_sso = (bool *) data;
+   if (*is_sso) {
+      /* Allow the removal of unused builtins in SSO */
+      return var->data.location > -1 && var->data.location < VARYING_SLOT_VAR0;
+   } else
+      return true;
+}
+
 /* First third of converting glsl_to_nir.. this leaves things in a pre-
  * nir_lower_io state, so that shader variants can more easily insert/
  * replace variables, etc.
@@ -342,15 +353,12 @@ st_nir_preprocess(struct st_context *st, struct gl_program *prog,
       NIR_PASS_V(nir, st_nir_add_point_size);
    }
 
-   /* ES has strict SSO validation rules for shader IO matching so we can't
-    * remove dead IO until the resource list has been built. Here we skip
-    * removing them until later. This will potentially make the IO lowering
-    * calls below do a little extra work but should otherwise have no impact.
-    */
-   if (!_mesa_is_gles(st->ctx) || !nir->info.separate_shader) {
-      nir_variable_mode mask = nir_var_shader_in | nir_var_shader_out;
-      nir_remove_dead_variables(nir, mask, NULL);
-   }
+   struct nir_remove_dead_variables_options opts;
+   bool is_sso = nir->info.separate_shader;
+   opts.can_remove_var_data = &is_sso;
+   opts.can_remove_var = &st_can_remove_varying_before_linking;
+   nir_variable_mode mask = nir_var_shader_in | nir_var_shader_out;
+   nir_remove_dead_variables(nir, mask, &opts);
 
    if (options->lower_all_io_to_temps ||
        nir->info.stage == MESA_SHADER_VERTEX ||
@@ -737,15 +745,6 @@ st_link_nir(struct gl_context *ctx,
 
    st_lower_patch_vertices_in(shader_program);
 
-   /* Linking the stages in the opposite order (from fragment to vertex)
-    * ensures that inter-shader outputs written to in an earlier stage
-    * are eliminated if they are (transitively) not used in a later
-    * stage.
-    */
-   for (int i = num_shaders - 2; i >= 0; i--) {
-      st_nir_link_shaders(linked_shader[i]->Program->nir,
-                          linked_shader[i + 1]->Program->nir);
-   }
    /* Linking shaders also optimizes them. Separate shaders, compute shaders
     * and shaders with a fixed-func VS or FS that don't need linking are
     * optimized here.
@@ -754,15 +753,42 @@ st_link_nir(struct gl_context *ctx,
       gl_nir_opts(linked_shader[0]->Program->nir);
 
    if (shader_program->data->spirv) {
+      /* Linking the stages in the opposite order (from fragment to vertex)
+       * ensures that inter-shader outputs written to in an earlier stage
+       * are eliminated if they are (transitively) not used in a later
+       * stage.
+       */
+      for (int i = num_shaders - 2; i >= 0; i--) {
+         st_nir_link_shaders(linked_shader[i]->Program->nir,
+                             linked_shader[i + 1]->Program->nir);
+      }
+
       static const gl_nir_linker_options opts = {
          true /*fill_parameters */
       };
       if (!gl_nir_link_spirv(&ctx->Const, shader_program, &opts))
          return GL_FALSE;
    } else {
-      if (!gl_nir_link_glsl(&ctx->Const, &ctx->Extensions,
+      if (!gl_nir_link_glsl(&ctx->Const, &ctx->Extensions, ctx->API,
                             shader_program))
          return GL_FALSE;
+
+      /* Linking the stages in the opposite order (from fragment to vertex)
+       * ensures that inter-shader outputs written to in an earlier stage
+       * are eliminated if they are (transitively) not used in a later
+       * stage.
+       */
+      for (int i = num_shaders - 2; i >= 0; i--) {
+         st_nir_link_shaders(linked_shader[i]->Program->nir,
+                             linked_shader[i + 1]->Program->nir);
+      }
+
+      /* Tidy up any left overs from the linking process for single shaders.
+       * For example varying arrays that get packed may have dead elements that
+       * can be now be eliminated now that array access has been lowered.
+       */
+      if (num_shaders == 1)
+         gl_nir_opts(linked_shader[0]->Program->nir);
    }
 
    for (unsigned i = 0; i < num_shaders; i++) {
diff --git a/src/panfrost/ci/traces-panfrost.yml b/src/panfrost/ci/traces-panfrost.yml
index ddc8502c418..cb5c655cc63 100644
--- a/src/panfrost/ci/traces-panfrost.yml
+++ b/src/panfrost/ci/traces-panfrost.yml
@@ -78,7 +78,7 @@ traces:
   - path: glmark2/bump:bump-render=height.trace
     expectations:
       - device: gl-panfrost-t860
-        checksum: 2efca26d7eb85d826276b30f3265153b
+        checksum: 73cb74446b0aefcfcf7b41d80eaed016
   - path: glmark2/bump:bump-render=high-poly.trace
     expectations:
       - device: gl-panfrost-t860