diff --git a/boards/cypress/cy8ckit_062_wifi_bt/doc/index.rst b/boards/cypress/cy8ckit_062_wifi_bt/doc/index.rst
index 515eb920c55..b11164e467d 100644
--- a/boards/cypress/cy8ckit_062_wifi_bt/doc/index.rst
+++ b/boards/cypress/cy8ckit_062_wifi_bt/doc/index.rst
@@ -146,7 +146,7 @@ CM4 core working FW for both cores should be written into Flash.  CM0+ FW
 should starts the CM4 core at one point using
 Cy_SysEnableCM4(CM4_START_ADDRESS); call.  CM4_START_ADDRESS is 0x10060000 in
 the current configuration. The CM0+/CM4 Flash/SRAM areas are defined in
-:zephyr_file:`dts/arm/cypress/psoc6.dtsi`.
+:zephyr_file:`dts/arm/infineon/cat1a/legacy/psoc6.dtsi`.
 
 Build the project for CM0+
 
diff --git a/boards/native/nrf_bsim/doc/nrf5340bsim.rst b/boards/native/nrf_bsim/doc/nrf5340bsim.rst
index 271e0db1bc1..7f43dc9093c 100644
--- a/boards/native/nrf_bsim/doc/nrf5340bsim.rst
+++ b/boards/native/nrf_bsim/doc/nrf5340bsim.rst
@@ -97,7 +97,7 @@ you can provide that image to the Zephyr build of the second image using
 You can also use :ref:`System build (sysbuild) <sysbuild>` to build your dual MCU executable.
 The best way to understand how, may be to look into how this is done in one of the examples
 in the tree. For example, for :ref:`the nrf53_sync_rtc sample <nrf53_sync_rtc_sample_build_bsim>`,
-:zephyr_file:`samples/boards/nrf/nrf53_sync_rtc/sysbuild.cmake`.
+:zephyr_file:`samples/boards/nordic/nrf53_sync_rtc/sysbuild.cmake`.
 
 
 .. note::
diff --git a/boards/nordic/nrf51dk/doc/index.rst b/boards/nordic/nrf51dk/doc/index.rst
index f5a2acbbcde..8cae453e2ed 100644
--- a/boards/nordic/nrf51dk/doc/index.rst
+++ b/boards/nordic/nrf51dk/doc/index.rst
@@ -1,4 +1,4 @@
-.. _nrf51dk_nrf51422:
+.. _nrf51dk_nrf51822:
 
 nRF51 DK
 ########
diff --git a/boards/others/stm32f103_mini/doc/index.rst b/boards/others/stm32f103_mini/doc/index.rst
index c19ded8a82f..0377a9b5952 100644
--- a/boards/others/stm32f103_mini/doc/index.rst
+++ b/boards/others/stm32f103_mini/doc/index.rst
@@ -76,7 +76,7 @@ The Zephyr stm32f103_mini board configuration supports the following hardware fe
 Other hardware features are not yet supported in this Zephyr port.
 
 The default configuration can be found in
-:zephyr_file:`boards/st/stm32f103_mini/stm32f103_mini_defconfig`
+:zephyr_file:`boards/others/stm32f103_mini/stm32f103_mini_defconfig`
 
 Connections and IOs
 ===================
diff --git a/boards/rakwireless/rak4631/doc/index.rst b/boards/rakwireless/rak4631/doc/index.rst
index 49055f67bf5..5d237f7bf71 100644
--- a/boards/rakwireless/rak4631/doc/index.rst
+++ b/boards/rakwireless/rak4631/doc/index.rst
@@ -71,7 +71,7 @@ The ``rak4631/nrf52840`` board configuration supports the following hardware fea
 +-----------+------------+----------------------+
 
 The default board configuration can be found in
-:zephyr_file:`boards/rak/rak4631/rak4631_nrf52840_defconfig`
+:zephyr_file:`boards/rakwireless/rak4631/rak4631_nrf52840_defconfig`
 
 Connections and IOs
 ===================
diff --git a/boards/silabs/radio_boards/slwrb4255a/doc/index.rst b/boards/silabs/radio_boards/slwrb4255a/doc/index.rst
index 50506431cf4..47cb5a15fbb 100644
--- a/boards/silabs/radio_boards/slwrb4255a/doc/index.rst
+++ b/boards/silabs/radio_boards/slwrb4255a/doc/index.rst
@@ -58,7 +58,7 @@ The board configuration supports the following hardware features:
 +-----------+------------+-------------------------------------+
 
 The default configuration can be found in
-:zephyr_file:`boards/silabs/radio_boards/slwrb4255/slwrb4255_defconfig`
+:zephyr_file:`boards/silabs/radio_boards/slwrb4255a/slwrb4255a_defconfig`
 
 Connections and IOs
 ===================
diff --git a/boards/silabs/radio_boards/slwrb4321a/doc/index.rst b/boards/silabs/radio_boards/slwrb4321a/doc/index.rst
index aa64ddc71d1..85237f7286a 100644
--- a/boards/silabs/radio_boards/slwrb4321a/doc/index.rst
+++ b/boards/silabs/radio_boards/slwrb4321a/doc/index.rst
@@ -60,7 +60,7 @@ features:
 +-----------+------------+-------------------------------------+
 
 The default configuration can be found in
-:zephyr_file:`boards/silabs/slwrb4321a/slwrb4321a_defconfig`
+:zephyr_file:`boards/silabs/radio_boards/slwrb4321a/slwrb4321a_defconfig`
 
 Other hardware features, including the WF200 WiFi transceiver, are
 currently not supported by the port.
diff --git a/boards/silabs/starter_kits/efm32wg_stk3800/doc/index.rst b/boards/silabs/starter_kits/efm32wg_stk3800/doc/index.rst
index 107bab8a518..d78df5eaaf1 100644
--- a/boards/silabs/starter_kits/efm32wg_stk3800/doc/index.rst
+++ b/boards/silabs/starter_kits/efm32wg_stk3800/doc/index.rst
@@ -50,7 +50,7 @@ The efm32wg_stk3800 board configuration supports the following hardware features
 +-----------+------------+-------------------------------------+
 
 The default configuration can be found in
-:zephyr_file:`boards/silabs/starter_kit/efm32wg_stk3800/efm32wg_stk3800_defconfig`
+:zephyr_file:`boards/silabs/starter_kits/efm32wg_stk3800/efm32wg_stk3800_defconfig`
 
 Other hardware features are currently not supported by the port.
 
diff --git a/boards/silabs/starter_kits/slstk3400a/doc/index.rst b/boards/silabs/starter_kits/slstk3400a/doc/index.rst
index fdfa5a4aab2..f3e3f6314c5 100644
--- a/boards/silabs/starter_kits/slstk3400a/doc/index.rst
+++ b/boards/silabs/starter_kits/slstk3400a/doc/index.rst
@@ -51,7 +51,7 @@ The efm32hg_slstk3400 board configuration supports the following hardware featur
 +-----------+------------+-------------------------------------+
 
 The default configuration can be found in
-:zephyr_file:`boards/silabs/starter_kit/slstk3400a/slstk3400a_defconfig`
+:zephyr_file:`boards/silabs/starter_kits/slstk3400a/slstk3400a_defconfig`
 
 Other hardware features are currently not supported by the port.
 
diff --git a/boards/snps/em_starterkit/doc/index.rst b/boards/snps/em_starterkit/doc/index.rst
index 28434f1d711..9fc53692b66 100644
--- a/boards/snps/em_starterkit/doc/index.rst
+++ b/boards/snps/em_starterkit/doc/index.rst
@@ -19,7 +19,7 @@ See also this URL for details about the board:
 The latest version of EM Starter Kit is 2.3, developer can upgrade from
 2.0/2.1/2.2 to 2.3 using latest firmware.
 The default configuration for EM Starter Kit boards can be found in
-:zephyr_file:`boards/snps/em_starterkit/em_starterkit_defconfig`.
+:zephyr_file:`boards/snps/em_starterkit/`.
 
 The default SoC for this board supported in Zephyr is the EM9D.
 This configuration is a Harvard Architecture, with a separate
diff --git a/boards/snps/nsim/arc_classic/doc/index.rst b/boards/snps/nsim/arc_classic/doc/index.rst
index 940d08f1b63..c3839dfc893 100644
--- a/boards/snps/nsim/arc_classic/doc/index.rst
+++ b/boards/snps/nsim/arc_classic/doc/index.rst
@@ -36,7 +36,7 @@ available configurations are listed below:
 .. _board_arc_nsim_prop_args_files:
 
 It is recommended to look at precise description of a particular sub-configuration in either
-``.props`` or ``.args`` files in :zephyr_file:`boards/snps/nsim/support/` directory to understand
+``.props`` or ``.args`` files in :zephyr_file:`boards/snps/nsim/arc_classic/support/` directory to understand
 which options are configured and so will be used on invocation of the simulator.
 
 In case of single-core configurations it would be ``.props`` file which contains configuration
@@ -52,14 +52,14 @@ simulation anyway).
    nSIM & MDB don't exactly match, so care should be taken).
 
 I.e. for the single-core ``nsim/nsim_hs5x`` platform there are
-:zephyr_file:`boards/snps/nsim/support/nsim_hs5x.props` and
-:zephyr_file:`boards/snps/nsim/support/mdb_hs5x.args`.
+:zephyr_file:`boards/snps/nsim/arc_classic/support/nsim_hs5x.props` and
+:zephyr_file:`boards/snps/nsim/arc_classic/support/mdb_hs5x.args`.
 
 For the multi-core configurations there is only ``.args`` file as the multi-core configuration
 can only be instantiated with help of MDB.
 
 I.e. for the multi-core ``nsim/nsim_hs5x/smp`` platform there is only
-:zephyr_file:`boards/snps/nsim/support/mdb_hs5x_smp.args`.
+:zephyr_file:`boards/snps/nsim/arc_classic/support/mdb_hs5x_smp.args`.
 
 .. warning::
    All nSIM/MDB configurations are used for demo and testing purposes. They are not meant to
@@ -87,7 +87,7 @@ Most board sub-configurations support building with both GNU and ARC MWDT toolch
 there might be exceptions from that, especially for newly added targets. You can check supported
 toolchains for the sub-configurations in the corresponding ``.yaml`` file.
 
-I.e. for the ``nsim/nsim_hs5x`` board we can check :zephyr_file:`boards/snps/nsim/nsim_nsim_hs5x.yaml`
+I.e. for the ``nsim/nsim_hs5x`` board we can check :zephyr_file:`boards/snps/nsim/arc_classic/nsim_nsim_hs5x.yaml`
 
 The supported toolchains are listed in ``toolchain:`` array in ``.yaml`` file, where we can find:
 
@@ -313,7 +313,7 @@ GNU & MWDT toolchain compiler options
 =====================================
 
 The hardware-specific compiler options are set in corresponding SoC cmake file. For ``nsim`` board
-it is :zephyr_file:`soc/snps/nsim/CMakeLists.txt`.
+it is :zephyr_file:`soc/snps/nsim/arc_classic/CMakeLists.txt`.
 
 For the GNU toolchain the basic configuration is set via ``-mcpu`` which is defined in generic code
 and based on the selected CPU model via Kconfig. It still can be forcefully set to required value
diff --git a/boards/snps/nsim/arc_v/doc/index.rst b/boards/snps/nsim/arc_v/doc/index.rst
index e7b1a48f1bb..a0bc41c2be7 100644
--- a/boards/snps/nsim/arc_v/doc/index.rst
+++ b/boards/snps/nsim/arc_v/doc/index.rst
@@ -17,7 +17,7 @@ Supported board targets for that platform are listed below:
 .. _board_nsim_arc_v_prop_files:
 
 It is recommended to look at precise description of a particular board target in ``.props``
-files in :zephyr_file:`boards/snps/nsim_arc_v/support/` directory to understand
+files in :zephyr_file:`boards/snps/nsim/arc_v/support/` directory to understand
 which options are configured and so will be used on invocation of the simulator.
 
 .. warning::
@@ -40,7 +40,7 @@ Most board targets support building with both GNU and ARC MWDT toolchains, howev
 there might be exceptions from that, especially for newly added targets. You can check supported
 toolchains for the board targets in the corresponding ``.yaml`` file.
 
-I.e. for the ``nsim_arc_v/rmx100`` board we can check :zephyr_file:`boards/snps/nsim_arc_v/nsim_arc_v_rmx100.yaml`
+I.e. for the ``nsim_arc_v/rmx100`` board we can check :zephyr_file:`boards/snps/nsim/arc_v/nsim_arc_v_rmx100.yaml`
 
 The supported toolchains are listed in ``toolchain:`` array in ``.yaml`` file, where we can find:
 
diff --git a/boards/sparkfun/thing_plus_matter_mgm240p/doc/index.rst b/boards/sparkfun/thing_plus_matter_mgm240p/doc/index.rst
index 4280345d8a2..2a3961884bf 100644
--- a/boards/sparkfun/thing_plus_matter_mgm240p/doc/index.rst
+++ b/boards/sparkfun/thing_plus_matter_mgm240p/doc/index.rst
@@ -81,7 +81,7 @@ means Pin number 2 on PORTA, as used in the board's datasheets and manuals.
 +-------+-------------+-------------------------------------+
 
 The default configuration can be found in
-:zephyr_file:`boards/silabs/sparkfun_thing_plus_matter_mgm240p/sparkfun_thing_plus_matter_mgm240p_defconfig`
+:zephyr_file:`boards/sparkfun/thing_plus_matter_mgm240p/sparkfun_thing_plus_matter_mgm240p_defconfig`
 
 System Clock
 ============
diff --git a/doc/hardware/porting/shields.rst b/doc/hardware/porting/shields.rst
index baf2a611fb7..6f3dff1be5f 100644
--- a/doc/hardware/porting/shields.rst
+++ b/doc/hardware/porting/shields.rst
@@ -12,7 +12,7 @@ Shield porting and configuration
 ********************************
 
 Shield configuration files are available in the board directory
-under :zephyr_file:`/boards/shields`:
+under :zephyr_file:`boards/shields`:
 
 .. code-block:: none
 
diff --git a/doc/services/logging/cs_stm.rst b/doc/services/logging/cs_stm.rst
index bf41ec3b25c..75a371dfd24 100644
--- a/doc/services/logging/cs_stm.rst
+++ b/doc/services/logging/cs_stm.rst
@@ -171,7 +171,7 @@ Stand-alone logging
 ===================
 
 Frontend is writing to STMESP registers. Message format is aligned with the on chip decoder
-in :zephyr_file:`subsys/logging/frontend/log_frontend_stmesp_demux.c`.
+in :zephyr_file:`subsys/logging/frontends/log_frontend_stmesp_demux.c`.
 
 ``Proxy`` is using Nordic specific peripheral (TBM) to get ETR buffer busyness and read and
 decode data and send human-readable data over UART. Nordic specific driver for ETR buffer is
diff --git a/samples/bluetooth/hci_spi/README.rst b/samples/bluetooth/hci_spi/README.rst
index 1276889e6a5..b29ab85b72c 100644
--- a/samples/bluetooth/hci_spi/README.rst
+++ b/samples/bluetooth/hci_spi/README.rst
@@ -23,9 +23,9 @@ for the HCI SPI slave device with compatible
 :dtcompatible:`zephyr,bt-hci-spi-slave`. This node sets an interrupt line to
 the host and associates the application with a SPI bus to use.
 
-See :zephyr_file:`boards/nrf51dk_nrf51422.overlay
-<samples/bluetooth/hci_spi/boards/nrf51dk_nrf51422.overlay>` in this sample
-directory for an example overlay for the :ref:`nrf51dk_nrf51422` board.
+See :zephyr_file:`boards/nrf51dk_nrf51822.overlay
+<samples/bluetooth/hci_spi/boards/nrf51dk_nrf51822.overlay>` in this sample
+directory for an example overlay for the :ref:`nrf51dk_nrf51822` board.
 
 You can then build this application and flash it onto your board in
 the usual way; see :ref:`boards` for board-specific building and
diff --git a/samples/bluetooth/hci_uart/README.rst b/samples/bluetooth/hci_uart/README.rst
index d07ddd4421e..ac909319a80 100644
--- a/samples/bluetooth/hci_uart/README.rst
+++ b/samples/bluetooth/hci_uart/README.rst
@@ -149,7 +149,7 @@ Check the :zephyr:code-sample:`ble_direction_finding_connectionless_rx` and the
 Using a USB CDC ACM UART
 ========================
 
-The sample can be configured to use a USB UART instead. See :zephyr_file:`samples/bluetooth/hci_uart/boards/nrf52840dongle_nrf52840.conf` and :zephyr_file:`samples/bluetooth/hci_uart/boards/nrf52840dongle_nrf52840.overlay`.
+The sample can be configured to use a USB UART instead. See :zephyr_file:`samples/bluetooth/hci_uart/boards/nrf52840dongle_nrf52840.conf`.
 
 Using the controller with the Zephyr host
 =========================================
diff --git a/samples/bluetooth/hci_uart_3wire/README.rst b/samples/bluetooth/hci_uart_3wire/README.rst
index effd001c760..6ebb9de32fd 100644
--- a/samples/bluetooth/hci_uart_3wire/README.rst
+++ b/samples/bluetooth/hci_uart_3wire/README.rst
@@ -149,7 +149,7 @@ Check the :zephyr:code-sample:`ble_direction_finding_connectionless_rx` and the
 Using a USB CDC ACM UART
 ========================
 
-The sample can be configured to use a USB UART instead. See :zephyr_file:`samples/bluetooth/hci_uart_3wire/boards/nrf52840dongle_nrf52840.conf` and :zephyr_file:`samples/bluetooth/hci_uart_3wire/boards/nrf52840dongle_nrf52840.overlay`.
+The sample can be configured to use a USB UART instead. See :zephyr_file:`samples/bluetooth/hci_uart_3wire/boards/nrf52840dongle_nrf52840.conf`.
 
 Using the controller with the Zephyr host
 =========================================
diff --git a/samples/boards/96boards/argonkey/microphone/README.rst b/samples/boards/96boards/argonkey/microphone/README.rst
index 64e70bc45ad..a62ceae084a 100644
--- a/samples/boards/96boards/argonkey/microphone/README.rst
+++ b/samples/boards/96boards/argonkey/microphone/README.rst
@@ -64,14 +64,14 @@ Five seconds of acquisition at a 16KHz sampling rate yields 80,000 16-bit sample
 The microphone PDM requested clock should lead the MP34DT05 driver to select an
 oversampling/decimation factor equal to 128, resulting in a 2.048MHz bit clock.
 
-See pcm and pdm configuration in file :zephyr_file:`samples/boards/96b_argonkey/microphone/src/main.c`.
+See pcm and pdm configuration in file :zephyr_file:`samples/boards/96boards/argonkey/microphone/src/main.c`.
 
 .. note:: It is possible to change the AUDIO_FREQ to 32000 acquiring only 2500 ms. In this
    case the oversampling/decimation factor will be 64.
 
 At the end of the acquisition the PCM data will be printed on the terminal
 emulator in either binary or ASCII format. The output is controlled by
-following macro, off by default, in :zephyr_file:`samples/boards/96b_argonkey/microphone/src/main.c`:
+following macro, off by default, in :zephyr_file:`samples/boards/96boards/argonkey/microphone/src/main.c`:
 
 * :c:macro:`PCM_OUTPUT_IN_ASCII`
 
diff --git a/samples/boards/96boards/argonkey/sensors/README.rst b/samples/boards/96boards/argonkey/sensors/README.rst
index 6f34235b451..1fd90973d65 100644
--- a/samples/boards/96boards/argonkey/sensors/README.rst
+++ b/samples/boards/96boards/argonkey/sensors/README.rst
@@ -20,7 +20,7 @@ in either one of the following two ways:
 - standalone mode, supplying 5V directly on P1 connector
 
 The user may select or unselect the sensors from
-:zephyr_file:`samples/boards/96b_argonkey/sensors/prj.conf`.
+:zephyr_file:`samples/boards/96boards/argonkey/sensors/prj.conf`.
 
 Please note that all sensor related code is conditionally compiled
 using the ``#ifdef`` directive, so this sample is supposed to always
diff --git a/samples/boards/nxp/s32/netc/README.rst b/samples/boards/nxp/s32/netc/README.rst
index ea2ee66ef1b..d9d2c501233 100644
--- a/samples/boards/nxp/s32/netc/README.rst
+++ b/samples/boards/nxp/s32/netc/README.rst
@@ -20,7 +20,7 @@ controls PSI) to allow users visualize the networking settings. Telnet shell
 and backend is also enabled.
 
 The source code for this sample application can be found at:
-:zephyr_file:`samples/boards/nxp_s32/netc`.
+:zephyr_file:`samples/boards/nxp/s32/netc`.
 
 Requirements
 ************
diff --git a/samples/drivers/led/led_strip/README.rst b/samples/drivers/led/led_strip/README.rst
index 703f27c7189..9c4efdc2c44 100644
--- a/samples/drivers/led/led_strip/README.rst
+++ b/samples/drivers/led/led_strip/README.rst
@@ -57,7 +57,7 @@ Note about thingy52
 The thingy52 has integrated NMOS transistors, that can be used instead of a level shifter.
 The I2S driver supports inverting the output to suit this scheme, using the ``out-active-low`` dts
 property. See the overlay file
-:zephyr_file:`samples/drivers/led_strip/boards/thingy52_nrf52832.overlay` for more detail.
+:zephyr_file:`samples/drivers/led/led_strip/boards/thingy52_nrf52832.overlay` for more detail.
 
 Building and Running
 ********************
diff --git a/samples/shields/x_nucleo_iks02a1/sensorhub/README.rst b/samples/shields/x_nucleo_iks02a1/sensorhub/README.rst
index 55597b90edd..56d1f9e5e00 100644
--- a/samples/shields/x_nucleo_iks02a1/sensorhub/README.rst
+++ b/samples/shields/x_nucleo_iks02a1/sensorhub/README.rst
@@ -32,7 +32,6 @@ and devicetree). See for example the :zephyr:board:`nucleo_f401re` board
 source code:
 
 - :zephyr_file:`boards/st/nucleo_f401re/nucleo_f401re.dts`
-- :zephyr_file:`boards/st/nucleo_f401re/pinmux.c`
 
 Please note that this sample can't be used with boards already supporting
 one of the sensors available on the shield (such as disco_l475_iot1)
diff --git a/samples/sysbuild/hello_world/README.rst b/samples/sysbuild/hello_world/README.rst
index 161df95beae..611d4a4781e 100644
--- a/samples/sysbuild/hello_world/README.rst
+++ b/samples/sysbuild/hello_world/README.rst
@@ -41,7 +41,7 @@ Here's an example to build and flash the sample for the
    :compact:
 
 The same can be achieved by using the
-:zephyr_file:`samples/basic/multitarget_hello_world/sample.yaml` setup:
+:zephyr_file:`samples/sysbuild/hello_world/sample.yaml` setup:
 
 .. zephyr-app-commands::
    :zephyr-app: samples/sysbuild/hello_world