Docs update model install instructions

book_source/01_introduction/00_introduction.Rmd

@@ -1 +1,5 @@
-# (PART) Introduction {-}
+# (PART) Introduction {-}
+
+This part introduces the PEcAn framework, its overall architecture, and
+the core concepts needed to understand how PEcAn supports ecosystem
+modeling workflows.

book_source/02_demos_tutorials_workflows/00_tutorials_demos_workflows.Rmd

@@ -1 +1,4 @@
 # (PART) Tutorials, Demos and How To's {-}
+
+This part contains hands-on tutorials, demonstrations, and step-by-step
+guides that show how to use PEcAn in practical modeling workflows.

book_source/03_topical_pages/00_topicalpages.Rmd

@@ -1,3 +1,4 @@
 # (PART) Topical Pages {-}
 
+This part groups related documentation pages by topic.
 

book_source/03_topical_pages/02_pecan_standards.Rmd

@@ -14,6 +14,7 @@ To aid in the conversion between PEcAn internal ISO_8601 standard and CF convent
 
 ### Meteorology Standards 
 
+
 #### Dimensions
 
 

book_source/03_topical_pages/03_pecan_xml.Rmd

@@ -435,22 +435,65 @@ The following are the most common types of inputs, along with their correspondin
 
 ##### `met`: Meteorological inputs {#xml-run-inputs-met}
 
--(Under construction. See the
--[`PEcAn.data.atmosphere` package documentation](https://pecanproject.github.io/package-documentation/develop/PEcAn.data.atmosphere/)
+See the `PEcAn.data.atmosphere` package documentation for more details.
+In particular, users working with meteorological inputs should focus on
+the data download functions and the `met2CF` conversion utilities, which
+handle retrieval of raw meteorological products and conversion to
+CF-compliant NetCDF files used by PEcAn.
 
 
-##### (Experimental) `soil`: Soil inputs {#xml-run-inputs-soil}
+##### `soil`: Soil inputs {#xml-run-inputs-soil}
 
-(Under construction. See the `PEcAn.data.land` package, located in `modules/data.land`, for more details).
+Soil inputs are handled through the `PEcAn.data.land` module.
+For full technical details, see the
+[PEcAn.data.land package documentation](https://pecan.ncsa.illinois.edu/pkgdocs/PEcAn.data.land/).
 
-##### (Experimental) `veg`: Vegetation initial conditions {#xml-run-inputs-veg}
+In practice, most PEcAn workflows do not rely on automated soil data
+processing at runtime. Instead, users typically preprocess soil data
+and provide standardized `soil.nc` files that are referenced directly
+in `pecan.xml`.
+
+Although automated soil processing is supported in principle, there are
+currently only two soil data products commonly used in PEcAn workflows:
+gSSURGO and SoilGrids.
+
+The `<soil>` element in `pecan.xml` is primarily used to specify paths to
+preprocessed soil inputs rather than to trigger on-the-fly data
+processing.
+
+Note that some models reference soil inputs using the `<soil>` tag,
+while others use `<soilphysics>`. This inconsistency is historical and
+can cause confusion; a future harmonization of these tags would be
+beneficial.
+
+
+##### `veg`: Vegetation initial conditions {#xml-run-inputs-veg}
 
 ##### `poolinitcond`: initial condition inputs {#xml-run-inputs-poolinitcond}
 * `source`: Data source of initial condition .rd veg files ex: NEON_veg, FIA.
 * `output`: This tag can only must match the cooresponding tag in the modeltypes_formats table that matches with your model type ex for SIPNET model tag is poolinitcond.
 * `ensemble`: Number of initial conditions ensemble member files ex: 30.
 
-(Under construction. Follow developments in the `PEcAn.data.land` package, located in `modules/data.land` in the source code).
+###### `phenology`
+
+Defines the timing of vegetation growth and dormancy, such as leaf-out and
+senescence. Phenology information allows PEcAn to determine when vegetation
+is actively growing and interacting with climate drivers.
+
+Phenology inputs are typically derived from external datasets and help align
+model simulations with observed seasonal behavior.
+
+###### `management`
+
+Specifies management activities applied to vegetation, such as planting,
+harvesting, fertilization, or irrigation. Management inputs allow PEcAn to
+represent human interventions that affect ecosystem processes.
+
+Management information may vary over time and is commonly linked to site- or
+crop-specific datasets.
+
+
+ (Follow developments in the `PEcAn.data.land` package, located in `modules/data.land` in the source code).
 
 ##### `pft.site` Multi-site site / PFT mapping
 

book_source/03_topical_pages/06_data/01_meteorology.Rmd

@@ -1,5 +1,20 @@
 # Available Meteorological Drivers {#met-drivers}
 
+- [ERA5](#era5)
+- [PRISM](#prism)
+- [Ameriflux](#ameriflux)
+- [NLDAS](#nldas)
+- [CRUNCEP](#cruncep)
+- [GLDAS](#gldas)
+- [CMIP5](#cmip5)
+- [Fluxnet2015](#fluxnet2015)
+- [ICOS Ecosystem Archive](#icos-ecosystem-archive)
+
+Note: This section highlights a subset of commonly used meteorological drivers and is not intended to be an exhaustive list.
+
+This chapter describes commonly used meteorological drivers supported by PEcAn and provides guidance on selecting an appropriate dataset.
+
+
 ## Ameriflux
 
 Scale: site

book_source/03_topical_pages/12_troubleshooting-pecan.Rmd

@@ -1,5 +1,20 @@
 # Troubleshooting and Debugging PEcAn
 
+This chapter provides guidance for diagnosing and resolving common
+issues encountered when running PEcAn workflows. Problems may arise
+from configuration errors, data availability issues, model failures,
+or system-level dependencies.
+
+Start with the general troubleshooting guidance below, then refer to
+specific sections for detailed solutions.
+
+## Common topics
+- [Workflow failures](#workflow-failures)
+- [Database issues](#database-issues)
+- [Model errors](#model-errors)
+- [Docker-related problems](#docker-issues)
+
+
 ## Cookies and pecan web pages
 
 You may need to disable cookies specifically for the pecan webserver in your browser. This is because your installation of php can include a 'PHPSESSID' that is quite long, and this can overflow the params field of the workflows table, depending on how long your hostname, model name, site name, etc are. 

book_source/03_topical_pages/93_installation/00_installation_index.Rmd

@@ -1,3 +1,8 @@
 # Installation details
 
+This page describes advanced installation options and system
+requirements for running PEcAn outside of Docker-based setups.
+Most users should follow the standard installation guide unless
+custom configurations are required.
+
 This chapter contains details about installing and maintaining the uncontainerized version of PEcAn on a virtual machine or a server. If you are running PEcAn inside of Docker, many of the particulars will be different and you should refer to the [docker](developer-workflows/docker-index.html) chapter instead of this one.

book_source/03_topical_pages/93_installation/03_install_OS/06_install_models/install_CLM4.5.Rmd

@@ -49,7 +49,7 @@ cd ~/carya/models/clm4_5_1_r085/scripts
 python runCLM.py --site US-UMB ––compset I1850CLM45CN --mach ubuntu --ccsm_input /home/carya/models/ccsm_inputdata --tstep 1 --nopointdata --coldstart --cpl_bypass --clean_build
 ```
 
-##### CLM Test Run
+**CLM Test Run**
 You will see a new directory in scripts:  US-UMB_I1850CLM45CN
 Enter this directory and run (you shouldn’t have to do this normally, but there is a bug with the python script and doing this ensures all files get to the right place):
 ```bash

book_source/03_topical_pages/93_installation/03_install_OS/06_install_models/install_SIPNET.Rmd

@@ -11,7 +11,7 @@ make
 sudo cp sipnet /usr/local/bin/sipnet.runk
 ```
 
-##### SIPNET testrun
+**SIPNET testrun**
 
 ```bash
 cd