Force exclude not working at reload

Title:
Force Exclude setting lost after restarting Embeetle

Operating system:
MX Linux

Embeetle version:
[enter version]

Project:
CH32V203 project

Steps to reproduce:

  1. Open the project.
  2. Right-click project/source/Samples/GPIO and select Force Exclude.
  3. Wait for the Source Analyzer to finish.
  4. Confirm that config/filetree.mk no longer contains the sample files.
  5. Close Embeetle completely.
  6. Reopen the project.
  7. The sample files are included again.

Expected result:
The Samples/GPIO folder remains force-excluded after restarting Embeetle.

Actual result:
The Source Analyzer adds the sample files back into config/filetree.mk.

Files added again:
project/source/Samples/GPIO/GPIO_Toggle/User/ch32v20x_it.c.o
project/source/Samples/GPIO/GPIO_Toggle/User/main.c.o
project/source/Samples/GPIO/GPIO_Toggle/User/system_ch32v20x.c.o

Mxlinux 25.2

Embeetle
version: 2.0.0 latest version: 2.0.0
date: 04 Feb 2026 latest date: 04 Feb 2026

~/.embeetle/home_window_output.txt is empty and this is my .beetle/output.txt

[VERSION-CHECK] Latest Embeetle version: 2.0.0 (Current: 2.0.0)
Change project status to busy
Change project linker status to waiting
Change project linker status to busy
Change project linker status to error
Change project status to ready
Remove error: multiply defined global symbol NMI_Handler at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/ch32v20x_it.c’ ( 991 )
Remove error: multiply defined global symbol HardFault_Handler at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/ch32v20x_it.c’ ( 1203 )
Change project status to busy
Change project linker status to waiting
Remove warning: format specifies type ‘int’ but the argument has type ‘uint32_t’ (aka ‘unsigned long’) at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/main.c’ ( 1532 )
Remove error: multiply defined global symbol main at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/main.c’ ( 1372 )
Remove error: multiply defined global symbol SystemCoreClock at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/system_ch32v20x.c’ ( 2253 )
Remove error: multiply defined global symbol AHBPrescTable at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/system_ch32v20x.c’ ( 3637 )
Remove error: multiply defined global symbol SystemInit at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/system_ch32v20x.c’ ( 5056 )
Remove error: multiply defined global symbol SystemCoreClockUpdate at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/Samples/GPIO/GPIO_Toggle/User/system_ch32v20x.c’ ( 5531 )
Remove error: multiply defined global symbol main at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/main.c’ ( 9988 )
Remove error: multiply defined global symbol SystemCoreClock at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 2686 )
Remove error: multiply defined global symbol AHBPrescTable at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 3637 )
Remove error: multiply defined global symbol SystemInit at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 5056 )
Remove error: multiply defined global symbol SystemCoreClockUpdate at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 5531 )
Remove error: multiply defined global symbol NMI_Handler at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/ch32v20x_it.c’ ( 1086 )
Remove error: multiply defined global symbol HardFault_Handler at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/ch32v20x_it.c’ ( 1298 )
Change project linker status to busy
Change project linker status to done
Remove error: multiply defined global symbol AHBPrescTable at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 3637 )
Remove error: multiply defined global symbol HardFault_Handler at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/ch32v20x_it.c’ ( 1298 )
Remove error: multiply defined global symbol NMI_Handler at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/ch32v20x_it.c’ ( 1086 )
Remove error: multiply defined global symbol SystemCoreClock at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 2686 )
Remove error: multiply defined global symbol SystemCoreClockUpdate at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 5531 )
Remove error: multiply defined global symbol SystemInit at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/system_ch32v20x.c’ ( 5056 )
Remove error: multiply defined global symbol main at ‘/home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a/source/User/main.c’ ( 9988 )
Change project status to ready

(MAKE) build -C build -f ../config/makefile TOOLPREFIX=(TOOLPREFIX)
FLASHTOOL=$(FLASHTOOL)

command = [‘/home/E480/embeetle/beetle_tools/gnu_make_4.2.1_64b/make’, ‘build’, ‘-C’, ‘build’, ‘-f’, ‘../config/makefile’, ‘TOOLPREFIX=/home/E480/embeetle/beetle_tools/gnu_riscv_xpack_toolchain_12.2.0_3_64b/bin/riscv-none-elf-’, ‘FLASHTOOL=/home/E480/embeetle/beetle_tools/openocd_wch_0.11.0_dev02415_64b/bin/openocd’]

cwd = /home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a

(MAKE) clean -C build -f ../config/makefile TOOLPREFIX=(TOOLPREFIX)
FLASHTOOL=$(FLASHTOOL)

command = [‘/home/E480/embeetle/beetle_tools/gnu_make_4.2.1_64b/make’, ‘clean’, ‘-C’, ‘build’, ‘-f’, ‘../config/makefile’, ‘TOOLPREFIX=/home/E480/embeetle/beetle_tools/gnu_riscv_xpack_toolchain_12.2.0_3_64b/bin/riscv-none-elf-’, ‘FLASHTOOL=/home/E480/embeetle/beetle_tools/openocd_wch_0.11.0_dev02415_64b/bin/openocd’]

cwd = /home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a

Change project status to busy
Change project linker status to waiting
Change project linker status to busy
Change project linker status to done
Change project status to ready

(MAKE) build -C build -f ../config/makefile TOOLPREFIX=(TOOLPREFIX)
FLASHTOOL=$(FLASHTOOL)

command = [‘/home/E480/embeetle/beetle_tools/gnu_make_4.2.1_64b/make’, ‘build’, ‘-C’, ‘build’, ‘-f’, ‘../config/makefile’, ‘TOOLPREFIX=/home/E480/embeetle/beetle_tools/gnu_riscv_xpack_toolchain_12.2.0_3_64b/bin/riscv-none-elf-’, ‘FLASHTOOL=/home/E480/embeetle/beetle_tools/openocd_wch_0.11.0_dev02415_64b/bin/openocd’]

cwd = /home/E480/Desktop/projects/tank-sensor/Software/mcu-software/tank-meter-rev-a