diff --git a/doc/user_guide/introduction_wfe/introduction.md b/doc/user_guide/introduction_wfe/introduction.md
index ba519bf..ea1aeb2 100644
--- a/doc/user_guide/introduction_wfe/introduction.md
+++ b/doc/user_guide/introduction_wfe/introduction.md
@@ -30,4 +30,17 @@ ctl/
 |---- expid.conf    -> model specifications
 ```
 
+Information: Inside `expid.conf`, variables set in the `master.conf`
+can be used (e.g. `MODEL_ID` set in `master.conf` could be used in
+`expid.conf` as `$MODEL_ID`).
 
+## Developer information
+
+Forks (i.e. SimExps) of the Workflow Engine should only change
+- `ctl/master.conf`
+- `ctl/expid.conf`
+- `.gitmodules`.
+
+All other changes should be applied to the main repository through
+Pull Requests (PRs) under
+<https://github.com/HPSCTerrSys/TSMP2_workflow-engine/pulls>.
diff --git a/doc/user_guide/usage_wfe/running.md b/doc/user_guide/usage_wfe/running.md
index ef78b1a..3345c95 100644
--- a/doc/user_guide/usage_wfe/running.md
+++ b/doc/user_guide/usage_wfe/running.md
@@ -1,7 +1,8 @@
 # Run experiment
 
 If you want to store your run directory files elsewhere than here, set a simulation ID (replace `MY-SIMULATION`) and make `${wfe_dir}/run` into a symlink pointing to your new directory.
-``` bash
+
+```bash
 cd ${wfe_dir}
 export sim_id=MY-SIMULATION
 export scratch_dir=$SCRATCH/$USER/$sim_id
@@ -13,12 +14,390 @@ ln -snf $scratch_dir/run run
 The configuration of the simulation is managed by two shell-based configure files besides the git submodules. `master.conf` for generic setting such as simulation time or model-id and `expid.conf` for doing component specific settings.
 
 Adapt resources and time in the setup-script.
-``` bash
+
+```bash
 cd ${wfe_dir}/ctl
 vi master.conf
 ```
 
 Start simulation
-``` bash
+
+```bash
 ./control_tsmp2.sh
 ```
+
+## master.conf
+
+The `master.conf` file contains general configuration settings for the
+workflow engine. It is located in `ctl/master.conf`.
+
+### Main Settings
+
+#### MODEL_ID
+
+Specifies which model components to use. Options include but are not
+restriced to:
+
+- `ParFlow` - ParFlow only
+- `ICON-eCLM` - ICON atmosphere with eCLM land surface
+- `ICON-eCLM-ParFlow` - Fully coupled system
+- `ICON` - ICON atmosphere only
+
+#### EXP_ID
+
+Experiment identifier (e.g., `"eur-11u"`). Used for naming and
+organizing simulation outputs.
+
+#### CASE_ID
+
+Optional identifier for specific cases within an experiment.
+
+#### conf_file
+
+Path to case-specific configuration file. If left empty, the system
+will look for `${ctl_dir}/expid.conf`.
+
+### Main Switches
+
+Each workflow stage has three boolean flags: `config`, `run`,
+`cleanup`.
+
+#### lpre
+
+Preprocessing stage switches: `( config run cleanup )`
+
+- `config`: Configure preprocessing
+- `run`: Execute preprocessing
+- `cleanup`: Clean up preprocessing files
+
+#### lsim
+
+Simulation stage switches: `( config run cleanup )`
+
+- `config`: Configure simulation
+- `run`: Execute simulation
+- `cleanup`: Clean up simulation files
+
+#### lpos
+
+Post-processing stage switches: `( config run cleanup )`
+
+- `config`: Configure post-processing
+- `run`: Execute post-processing
+- `cleanup`: Clean up post-processing files
+
+#### lvis
+
+Visualization stage switches: `( config run cleanup )`
+
+- `config`: Configure visualization
+- `run`: Execute visualization
+- `cleanup`: Clean up visualization files
+
+### Time Information
+
+#### cpltsp_atmsfc
+
+Coupling time step between atmosphere and surface (eCLM timestep) in
+seconds. Default: `900`.
+
+#### cpltsp_sfcss
+
+Coupling time step between surface and subsurface (ParFlow timestep)
+in seconds. Default: `900`.
+
+#### simlength
+
+Length of each simulation step (e.g., `"1 day"`, `"23 hours"`).
+
+#### startdate
+
+Start date of the simulation in ISO 8601 format (e.g.,
+`"2017-07-01T00:00Z"`).
+
+#### inidate
+
+Initial date for the entire simulation in ISO 8601 format. Default:
+same as `startdate`.
+
+#### numsimstep
+
+Number of simulation steps.
+
+Total simulation time = `numsimstep * simlength`.
+
+Each simulation step is a queued job on the machine. The next job is
+only executed once the previous is done.
+
+### Mail Notification
+
+#### mailtype
+
+Email notification trigger for SLURM jobs. Options: `NONE`, `BEGIN`,
+`END`, `FAIL`, `REQUEUE`, `ALL`.
+
+#### mailaddress
+
+Email address for job notifications. Leave empty if `mailtype=NONE`.
+
+### User Settings
+
+#### prevjobid
+
+Previous job ID for job chaining. Leave empty by default; system will
+manage this automatically.
+
+#### npnode
+
+Number of cores per node. Leave empty to use machine defaults.
+
+#### partition
+
+Compute partition to use. Leave empty to use machine defaults.
+
+#### account
+
+Compute account for billing. If not set, `$BUDGET_ACCOUNTS` or `slts`
+will be used.
+
+### Wallclock Times
+
+Wallclock time limits for each workflow stage in `hh:mm:ss` format.
+
+#### pre_wallclock
+
+Time limit for preprocessing jobs (e.g., `00:35:00`).
+
+#### sim_wallclock
+
+Time limit for simulation jobs (e.g., `00:25:00`).
+
+#### pos_wallclock
+
+Time limit for post-processing jobs (e.g., `00:05:00`).
+
+#### vis_wallclock
+
+Time limit for visualization jobs (e.g., `00:05:00`).
+
+### File/Directory Paths
+
+#### tsmp2_dir
+
+Path to TSMP2 directory. Uses `$TSMP2_DIR` environment variable.
+
+#### tsmp2_install_dir
+
+Path to TSMP2 installation directory. Leave empty to use default.
+
+#### tsmp2_env
+
+Path to TSMP2 environment file. Leave empty to use default.
+
+### Node Allocation
+
+Number of nodes allocated to each model component. Components not
+indicated in `MODEL_ID` will have their node count set to zero.
+
+#### ico_node
+
+Number of nodes for ICON atmosphere component. Default: `3`.
+
+#### clm_node
+
+Number of nodes for eCLM land surface component. Default: `1`.
+
+#### pfl_node
+
+Number of nodes for ParFlow subsurface component. Default: `2`.
+
+### Debug and Logging
+
+#### debugmode
+
+If set to `true`, no job submission is carried out. Works only for
+`config` steps.
+
+Useful for testing configuration without running jobs.
+
+Useful for running single tasks, e.g. namelist creation.
+
+#### joblog
+
+If set to `true`, job status will be logged. Default: `true`.
+
+## expid.conf
+
+The `expid.conf` file contains component-specific configuration
+settings for the workflow engine. It is located in `ctl/expid.conf` by
+default, or at the path specified by `conf_file` in `master.conf`.
+
+The file is organized into sections for each workflow stage
+(preprocessing, simulation, post-processing, visualization) and
+further subdivided by component.
+
+### Preprocessing Configuration
+
+#### [pre_config_clm]
+
+Configuration settings for eCLM preprocessing stage. Currently empty
+in the default configuration.
+
+### Simulation Configuration
+
+#### [sim_config_general]
+
+General simulation configuration settings applicable across all
+components. Currently empty in the default configuration.
+
+#### [sim_config_icon]
+
+ICON atmosphere component configuration.
+
+##### icon_numioprocs
+
+Number of I/O processors for ICON. Controls how many processes handle
+file output operations (e.g., `3`).
+
+##### fname_dwdFG
+
+Filename for DWD first guess data used by ICON (e.g.,
+`dwdFG_R13B05_DOM01.nc`).
+
+##### fname_icondomain
+
+Filename for ICON domain grid file (e.g., `europe011_DOM01.nc`).
+
+##### fname_iconextpar
+
+Filename for ICON external parameters including tiles (e.g.,
+`external_parameter_icon_europe011_DOM01_tiles.nc`).
+
+##### fname_iconghgforc
+
+Filename for greenhouse gas forcing data (e.g.,
+`bc_greenhouse_rcp45_1765-2500.nc`). Used for climate scenario
+simulations.
+
+#### [sim_config_clm]
+
+eCLM land surface component configuration.
+
+For eCLM namelist definitions (derived from CLM5.0 if not declared
+otherwise), see
+https://docs.cesm.ucar.edu/models/cesm2/settings/current/clm5_0_nml.html
+
+##### geo_dir_clm
+
+Directory path for eCLM static geographical input files (domain file,
+surface data, topography, etc.). Default: `${geo_dir}/eclm/static`
+(e.g., `./input_clm`).
+
+##### clm_frc_dir
+
+Directory path for eCLM atmospheric forcing data. Default:
+`${frc_dir}/eclm/forcing/` (e.g., `./forcings`).
+
+##### domainfile_clm
+
+Domain file for eCLM grid definition. Specifies land/lake mask and
+grid structure (e.g.,
+`domain.lnd.ICON-11_ICON-11.230302_landlake_halo.nc`).
+
+##### surffile_clm
+
+Surface data file for eCLM containing vegetation, soil properties, and
+land use (e.g.,
+`surfdata_ICON-11_hist_16pfts_Irrig_CMIP6_simyr2000_c230302_gcvurb-pfsoil_halo.nc`).
+
+##### fini_clm
+
+Path to eCLM restart file for continuing simulations. Used when
+`startdate` differs from `inidate`. Default: automatically determined
+from previous simulation restart directory (e.g.,
+`./input_clm/FSpinup_300x300_NRW.clm2.r.2222-01-01-00000.nc`).
+
+##### clm_tsp
+
+eCLM timestep in seconds.
+
+Default: value of `cpltsp_atmsfc` from `master.conf` (e.g., `1800` for
+30-minute timestep).
+
+##### clmoutvar
+
+Comma-separated list of eCLM output variables.
+
+Sets `hist_fincl1` in eCLM's `lnd_in` namelist.
+
+##### clmoutfrq
+
+eCLM history output frequency in hours (negative values).
+
+Sets `hist_nhtfrq` in eCLM's `lnd_in` namelist.
+
+##### clmoutmfilt
+
+Maximum number of time samples per eCLM history file.
+
+Sets `hist_mfilt` in eCLM's `lnd_in` namelist.
+
+#### [sim_config_parflow]
+
+ParFlow subsurface component configuration.
+
+##### pfl_ngx
+
+Number of grid cells in x-direction for ParFlow domain (e.g., `444`).
+
+##### pfl_ngy
+
+Number of grid cells in y-direction for ParFlow domain (e.g., `432`).
+
+##### pfl_mask
+
+Filename for ParFlow solid file mask defining inactive cells (e.g.,
+`PfbMask4SolidFile_eCLM.pfsol`).
+
+##### pfloutmfilt
+
+Output frequency multiplier for ParFlow files. Controls how often
+output is written (e.g., `24` means every 24 timesteps).
+
+##### pfltsfilerst
+
+Timestep file index for ParFlow restart files. Typically set to
+`$((pfloutmfilt - 1))` to align with output frequency.
+
+#### [sim_config_oas]
+
+OASIS coupler configuration for component coupling.
+
+##### icon_ncg
+
+Number of grid cells for ICON in OASIS coupler (e.g., `189976`). Must
+match ICON grid definition.
+
+##### clm_ngx
+
+Number of grid cells in x-direction for eCLM in OASIS coupler (e.g.,
+`189976`). For unstructured grids, represents total cell count.
+
+##### clm_ngy
+
+Number of grid cells in y-direction for eCLM in OASIS coupler. For
+unstructured grids, set to `1`.
+
+### Post-processing Configuration
+
+#### [pos_config_*]
+
+Configuration settings for post-processing stage. Currently empty in
+the default configuration.
+
+### Visualization Configuration
+
+#### [vis_config_*]
+
+Configuration settings for visualization stage. Currently empty in the
+default configuration.