Fix build system regressions

This commit consolidates multiple build system fixes:
1. DTB compilation regression
   - Fixed unconditional DTB build in user-space mode
   - Fixed WebAssembly build missing DTB dependencies
   - Fixed DTB not being built on macOS-arm64 for SYSTEM mode
2. Makefile syntax error
   - Fixed TAB characters before $(warning) in mk/toolchain.mk
   - This prevented entire Makefile from parsing correctly
3. emcc configuration pollution
   - Fixed .config persistence causing ENABLE_SYSTEM=1 to leak
   - Added distclean before emcc builds to ensure clean state
4. Ubuntu ARM64 apt-get failures
   - Exponential backoff: 30s, 60s delays (mirror sync needs time)
   - Detect "Mirror sync in progress" in addition to fetch failures
   - Fallback with --fix-broken install if apt install fails
   - Reduced retries from 5 to 3 (longer delays are more effective)

Author: jserv

.github/workflows/main.yml

@@ -135,14 +135,15 @@ jobs:
     - name: default build using emcc
       if: success()
       run: |
+            make distclean
             make CC=emcc ENABLE_JIT=0 $PARALLEL
 
     - name: default build for system emulation using emcc
       if: success()
       run: |
             make distclean
             make CC=emcc ENABLE_SYSTEM=1 ENABLE_JIT=0 $PARALLEL
-            make distclean ENABLE_SYSTEM=1
+            make distclean
 
     - name: Build with various optimization levels
       if: success()
@@ -301,8 +302,28 @@ jobs:
         githubToken: ${{ github.token }}
         # No 'sudo' is available
         install: |
-          apt update -qq
-          apt install -yqq make git curl wget clang libsdl2-dev libsdl2-mixer-dev lsb-release software-properties-common gnupg bc
+          # Retry apt update with exponential backoff for mirror sync issues
+          # apt update returns 0 even with partial failures, so check logs
+          for i in 1 2 3; do
+            apt update -qq --allow-releaseinfo-change 2>&1 | tee /tmp/apt-update.log
+            if ! grep -q "Failed to fetch\|Hash Sum mismatch\|Mirror sync in progress" /tmp/apt-update.log; then
+              echo "apt update succeeded on attempt $i"
+              break
+            fi
+            if [ $i -lt 3 ]; then
+              delay=$((i * 30))
+              echo "apt update attempt $i had errors, waiting ${delay}s for mirror sync..."
+              sleep $delay
+            else
+              echo "Warning: Proceeding with partial package lists after 3 attempts..."
+              echo "This is usually safe - required packages are likely available"
+            fi
+          done
+          apt install -yqq make git curl wget clang libsdl2-dev libsdl2-mixer-dev lsb-release software-properties-common gnupg bc || {
+            echo "Warning: apt install had issues, retrying with apt --fix-broken install"
+            apt --fix-broken install -yqq
+            apt install -yqq make git curl wget clang libsdl2-dev libsdl2-mixer-dev lsb-release software-properties-common gnupg bc
+          }
           which wget || echo "WARNING: wget not found after installation"
         # FIXME: gcc build fails on Aarch64/Linux hosts
         env: |
@@ -311,7 +332,17 @@ jobs:
         run: |
           # Verify and install wget if needed (workaround for install step issues)
           if ! command -v wget > /dev/null 2>&1; then
-            apt update -qq && apt install -yqq wget
+            for i in 1 2; do
+              apt update -qq --allow-releaseinfo-change 2>&1 | tee /tmp/apt-update-wget.log
+              if ! grep -q "Failed to fetch\|Hash Sum mismatch\|Mirror sync in progress" /tmp/apt-update-wget.log; then
+                break
+              fi
+              if [ $i -lt 2 ]; then
+                echo "apt update retry $i had errors, waiting 30s for mirror sync..."
+                sleep 30
+              fi
+            done
+            apt install -yqq wget || echo "Warning: wget install failed, may affect later steps"
           fi
           git config --global --add safe.directory ${{ github.workspace }}
           git config --global --add safe.directory ${{ github.workspace }}/src/softfloat
@@ -435,14 +466,15 @@ jobs:
      - name: default build using emcc
        if: success()
        run: |
+             make distclean
              make CC=emcc ENABLE_JIT=0 $PARALLEL
 
      - name: default build for system emulation using emcc
        if: success()
        run: |
              make distclean
              make CC=emcc ENABLE_SYSTEM=1 ENABLE_JIT=0 $PARALLEL
-             make distclean ENABLE_SYSTEM=1
+             make distclean
 
      - name: check + tests
        if: success()
@@ -499,14 +531,14 @@ jobs:
                fi
              done
 
-    - name: JIT debug test
-      env:
-        CC: ${{ steps.install_cc.outputs.cc }}
-      run: |
-            # Run JIT tests with debug mode to catch register allocation and cache coherency issues
-            make distclean && make ENABLE_JIT=1 ENABLE_JIT_DEBUG=1 check $PARALLEL
-            make distclean && make ENABLE_EXT_C=0 ENABLE_JIT=1 ENABLE_JIT_DEBUG=1 check $PARALLEL
-      if: ${{ always() }}
+     - name: JIT debug test
+       env:
+         CC: ${{ steps.install_cc.outputs.cc }}
+       run: |
+             # Run JIT tests with debug mode to catch register allocation and cache coherency issues
+             make distclean && make ENABLE_JIT=1 ENABLE_JIT_DEBUG=1 check $PARALLEL
+             make distclean && make ENABLE_EXT_C=0 ENABLE_JIT=1 ENABLE_JIT_DEBUG=1 check $PARALLEL
+       if: ${{ always() }}
 
      - name: undefined behavior test
        if: (success() || failure()) && steps.install_cc.outputs.cc == 'clang'  # gcc on macOS/arm64 does not support sanitizers

Makefile

@@ -392,7 +392,7 @@ DTB_DEPS := $(BUILD_DTB) $(BUILD_DTB2C)
 endif
 endif
 
-all: config $(DTB_DEPS) $(BUILD_DTB) $(BUILD_DTB2C) $(BIN)
+all: config $(DTB_DEPS) $(BIN)
 
 OBJS := \
     map.o \
@@ -437,7 +437,7 @@ $(OUT):
 
 $(BIN): $(OBJS) $(DEV_OBJS) | $(OUT)
 	$(VECHO) "  LD\t$@\n"
-	$(Q)$(CC) -o $@ $(CFLAGS_emcc) $^ $(LDFLAGS)
+	$(Q)$(CC) -o $@ $(CFLAGS_emcc) $(filter-out %.dtb %.h,$^) $(LDFLAGS)
 
 $(CONFIG_FILE): FORCE
 	$(Q)mkdir -p $(OUT)

mk/toolchain.mk

@@ -22,10 +22,10 @@ ifneq ($(shell $(CC) --version | head -n 1 | grep emcc),)
                 $(warning $(SDL_MUSIC_CANNOT_PLAY_WARNING))
             endif
         else
-	    $(warning $(SDL_MUSIC_CANNOT_PLAY_WARNING))
+        $(warning $(SDL_MUSIC_CANNOT_PLAY_WARNING))
         endif
     else
-	$(warning $(SDL_MUSIC_CANNOT_PLAY_WARNING))
+        $(warning $(SDL_MUSIC_CANNOT_PLAY_WARNING))
     endif
 
     # see commit 165c1a3 of emscripten

mk/wasm.mk

@@ -166,3 +166,21 @@ start-web: $(start_web_deps)
 .PHONY: check-demo-dir-exist start-web
 
 endif
+
+# For SYSTEM mode, DTB needs to be built regardless of whether we're using emcc
+# DTB is only built when SYSTEM=1 and ELF_LOADER=0
+ifeq ($(call has, SYSTEM), 1)
+ifeq ($(call has, ELF_LOADER), 0)
+# Add DTB as dependency for compilation stages
+# This is used by mk/system.mk for device object files
+deps_emcc += $(BUILD_DTB) $(BUILD_DTB2C)
+
+# For emcc builds: ensure DTB exists before emcc embeds it
+# Make BIN directly depend on DTB files as regular prerequisites
+# This will cause them to be built, but they'll also be passed to the linker
+# We need to filter them out in the linker command
+ifeq ("$(CC_IS_EMCC)", "1")
+$(BIN): $(BUILD_DTB) $(BUILD_DTB2C)
+endif
+endif
+endif