doc: Add Thingy:53 pairing known issue for v2.1.0

Document a known issue discovered during v2.1.0 release testing where
the Thingy:53 board (thingy53_nrf5340_cpuapp) cannot complete Bluetooth
LE pairing successfully.

Ref: NCSDK-39018

Signed-off-by: Piotr Osowski <piotr.osowski@nordicsemi.no>

Author: pioso-dev

doc/known_issues.rst

@@ -24,17 +24,39 @@ A known issue can list one or both of the following entries:
 List of known issues for v2.1.0 release
 ***************************************
 
-There are no reported known issues for the v2.1.0 release.
+NCSDK-39293: Thingy:53 cannot pair successfully over Bluetooth LE
+  When using the Thingy:53 board, the device cannot complete Bluetooth LE pairing successfully.
+
+  **Affected platforms:** Thingy:53
+
+NCSDK-39297: CMake duplicates the board configuration directory in ``CONF_FILE`` paths when used with the nRF Connect for VS Code GUI
+  The application's CMake setup sets ``APPLICATION_CONFIG_DIR`` to ``configuration/<board>_<qualifiers>/``, which causes Zephyr to resolve ``CONF_FILE`` relative to that directory instead of the application root.
+  As a result, ``CONF_FILE`` must be set to a file name only (for example, :file:`prj_release.conf`), and must not include the ``configuration/<board>_<qualifiers>/`` prefix.
+
+  However, the Kconfig fragment picker in the nRF Connect for VS Code extension inserts the path relative to the application root, for example::
+
+    configuration/nrf54l15tag_nrf54l15_cpuapp/prj_release.conf
+
+  CMake then prepends ``APPLICATION_CONFIG_DIR`` again, the board configuration sub-path is duplicated, and the build fails with an error similar to::
+
+    CMake Error at .../zephyr/cmake/modules/kconfig.cmake:318 (message):
+      File not found:
+      .../applications/gesture_recognition/configuration/nrf54l15tag_nrf54l15_cpuapp/configuration/nrf54l15tag_nrf54l15_cpuapp/prj.conf
+
+  **Workaround:** Set ``CONF_FILE`` to the file name only, relative to ``APPLICATION_CONFIG_DIR``, and omit the ``configuration/<board>_<qualifiers>/`` prefix.
+  On the command line, pass the file name directly, for example::
+
+      west build -b nrf54l15tag/nrf54l15/cpuapp -- -DCONF_FILE=prj_release.conf
 
 List of known issues for v2.0.0 release
 ***************************************
 
 DRGN-27788: Bluetooth LE disables RRAM low-latency mode when using AXON NPU and Bluetooth LE simultaneously on the nRF54LM20B SoC
-  When running AXON and Bluetooth LE together on nRF54LM20B, Bluetooth LE might disable RRAM low-latency mode during radio activity, which may slow or corrupt an ongoing inference. 
+  When running AXON and Bluetooth LE together on nRF54LM20B, Bluetooth LE might disable RRAM low-latency mode during radio activity, which may slow or corrupt an ongoing inference.
   MPSL sets STANDBY mode in ``NRF_RRAMC->POWER.LOWPOWERCONFIG`` at the start of each radio slot and restores the application init value at the end.
   In a power-optimized application, if the radio slot ends while an inference is running on Axon, the low-power (``NRF_RRAMC_LP_POWER_OFF``) value will be forced by MPSL, slowing down the rest of the inference.
 
   **Workaround:** Use ``CONFIG_MPSL_FORCE_RRAM_ON_ALL_THE_TIME`` to keep RRAM permanently in STANDBY mode.
   This setting increases power consumption but ensures reliable performance.
-  
+
   **Affected platforms:** nRF54LM20B SoC