diff --git a/DESCRIPTION b/DESCRIPTION
index 9958ccf4..c01a6884 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,9 +18,11 @@ Imports:
     gridExtra,
     gt,
     naniar,
+    nmfspalette,
     officer,
     openxlsx,
     prodlim,
+    r4ss,
     satf,
     stats,
     stringr,
@@ -40,7 +42,8 @@ VignetteBuilder:
     knitr
 Remotes:
     nmfs-ost/satf,
-    r4ss/r4ss
+    r4ss/r4ss,
+    nmfs-fish-tools/nmfspalette
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8
diff --git a/R/add_base_section.R b/R/add_base_section.R
index 0fee568f..e0edf650 100644
--- a/R/add_base_section.R
+++ b/R/add_base_section.R
@@ -11,12 +11,12 @@ add_base_section <- function(custom_sections) {
   section_list <- list()
   for (i in 1:length(sec_sel)) {
     sec_file <- grep(
-      custom_sections = list.files(system.file("templates", "skeleton", package = "asar")),
+      list.files(system.file("templates", "skeleton", package = "asar")),
       pattern = sec_sel[i],
       value = TRUE
     )
     if (identical(sec_file, character(0))) stop("One or more section name(s) does not exist. Please check the spelling or if you are tring to add a section that is not in the default template, please use parameter 'custom_sections' and refer to documentation. To check which sections are in the base template please run list.files(system.file('templates', 'skeleton', package = 'ASAR')) in your console")
-    sec_file -> section_list[i]
+    sec_file -> section_list[[i]]
   }
-  section_list
+  as.list(unlist(section_list))
 }
diff --git a/R/add_section.R b/R/add_section.R
index f9271b5d..bc61cea0 100644
--- a/R/add_section.R
+++ b/R/add_section.R
@@ -26,7 +26,7 @@ add_section <- function(
   # after-section
   # in-section (will always append to the end of the section)
   for (i in 1:length(new_section)) {
-    section_i_name <- paste0(gsub(" ", "_", new_section[i]), ".qmd")
+    section_i_name <- paste0(gsub(" ", "_", tolower(new_section[i])), ".qmd")
     local_section <- forstringr::str_extract_part(section_location[i], "-", before = FALSE)
     local_section_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = FALSE)
 
@@ -39,7 +39,7 @@ add_section <- function(
     }
 
     section_i <- paste0(
-      "## ", stringr::str_to_title(sub("_", " ", new_section[i])), "\n",
+      "## ", stringr::str_to_title(sub("_", " ", tolower(new_section[i]))), "\n",
       "\n",
       "[Insert text here]", "\n",
       "\n",
@@ -51,9 +51,9 @@ add_section <- function(
       custom_sections <- append(custom_sections, section_i_name, after = (which(grepl(local_section, custom_sections)) - 1))
     } else if (locality == "after") {
       if (locality %in% locality_prev & local_section %in% local_section_prev) {
-        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(gsub(" ", "_", new_section[i - 1]), custom_sections)))
+        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(gsub(" ", "_", tolower(new_section[i - 1])), custom_sections)))
       } else {
-        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(local_section, custom_sections)))
+        custom_sections <- append(custom_sections, section_i_name, after = max(which(grepl(local_section, custom_sections))))
       }
     } else if (locality == "in") {
       stop("No available option for adding a new section 'in' another quarto document.", call. = FALSE)
diff --git a/R/create_figures_doc.R b/R/create_figures_doc.R
index bd30b62f..e0f1301b 100644
--- a/R/create_figures_doc.R
+++ b/R/create_figures_doc.R
@@ -28,6 +28,7 @@ create_figures_doc <- function(resdir = NULL,
       add_chunk(
         paste0("satf::plot_recruitment(dat = '", resdir, "/", model_results, "', model = '", model, "')"),
         label = "recruitment",
+        eval = "false",
         add_option = TRUE,
         chunk_op = "fig-cap: 'this is the caption for the figure.'"
       ),
@@ -41,7 +42,7 @@ create_figures_doc <- function(resdir = NULL,
     )
     figures_doc <- paste0(
       figures_doc,
-      add_chunk(plot_code, label = "spawn_bio"),
+      add_chunk(plot_code, label = "spawn_bio", eval = "false"),
       "\n"
     )
   } else {
@@ -49,5 +50,5 @@ create_figures_doc <- function(resdir = NULL,
   }
 
   # Save tables doc to template folder
-  utils::capture.output(cat(figures_doc), file = paste0(subdir, "/", "figures.qmd"), append = FALSE)
+  utils::capture.output(cat(figures_doc), file = paste0(subdir, "/", "09_figures.qmd"), append = FALSE)
 }
diff --git a/R/create_tables_doc.R b/R/create_tables_doc.R
index 647684b0..c1438683 100644
--- a/R/create_tables_doc.R
+++ b/R/create_tables_doc.R
@@ -26,7 +26,8 @@ create_tables_doc <- function(resdir = NULL,
         paste0(
           "satf::table_indices(dat = '", resdir, "/", model_results, "', model = '", model, "')"
         ),
-        label = "indices"
+        label = "indices",
+        eval = "false"
       )
     )
 
@@ -44,5 +45,7 @@ create_tables_doc <- function(resdir = NULL,
   }
 
   # Save tables doc to template folder
-  utils::capture.output(cat(tables_doc), file = paste0(subdir, "/", "tables.qmd"), append = FALSE)
+  utils::capture.output(cat(tables_doc),
+                        file = paste0(subdir, "/", "08_tables.qmd"),
+                        append = FALSE)
 }
diff --git a/R/create_template.R b/R/create_template.R
index 6781c0ff..7ab0c780 100644
--- a/R/create_template.R
+++ b/R/create_template.R
@@ -276,7 +276,7 @@ create_template <- function(
             "### Tables \n \n",
             "Please refer to the `satf` package downloaded from remotes::install_github('nmfs-ost/satf') to add premade tables."
           )
-          utils::capture.output(cat(tables_doc), file = fs::path(subdir, "tables.qmd"), append = FALSE)
+          utils::capture.output(cat(tables_doc), file = fs::path(subdir, "08_tables.qmd"), append = FALSE)
           warning("Results file or model name not defined.")
         }
       } else {
@@ -284,7 +284,7 @@ create_template <- function(
           "### Tables \n \n",
           "Please refer to the `satf` package downloaded from remotes::install_github('nmfs-ost/satf') to add premade figures"
         )
-        utils::capture.output(cat(tables_doc), file = fs::path(subdir, "tables.qmd"), append = FALSE)
+        utils::capture.output(cat(tables_doc), file = fs::path(subdir, "08_tables.qmd"), append = FALSE)
       }
       # Create figures qmd
       if (include_figures) {
@@ -298,12 +298,12 @@ create_template <- function(
           )
         } else {
           figures_doc <- paste0("## Figures \n")
-          utils::capture.output(cat(figures_doc), file = fs::path(subdir, "figures.qmd"), append = FALSE)
+          utils::capture.output(cat(figures_doc), file = fs::path(subdir, "09_figures.qmd"), append = FALSE)
           warning("Results file or model name not defined.")
         }
       } else {
         figures_doc <- paste0("## Figures \n")
-        utils::capture.output(cat(figures_doc), file = fs::path(subdir, "figures.qmd"), append = FALSE)
+        utils::capture.output(cat(figures_doc), file = fs::path(subdir, "09_figures.qmd"), append = FALSE)
       }
 
       # Part I
@@ -441,6 +441,7 @@ create_template <- function(
         # Date
         "date: today", "\n",
         "lang: en \n",
+        "keep-tex: true \n"
       )
 
       # Add species image on title page
@@ -569,32 +570,38 @@ create_template <- function(
       if (custom == FALSE) {
         sections <- add_child(
           c(
-            "executive_summary.qmd",
-            "introduction.qmd",
-            "data.qmd",
-            "modeling_approach.qmd",
-            "results.qmd",
-            "projections.qmd",
-            "discussion.qmd",
-            "acknowledgments.qmd",
-            "references.qmd",
-            "tables.qmd",
-            "figures.qmd",
-            "appendix.qmd"
+            "01_executive_summary.qmd",
+            "02_introduction.qmd",
+            "03_data.qmd",
+            "04a_assessment-configuration.qmd",
+            "04b_assessment-results.qmd",
+            "04c_assessment-sensitivity.qmd",
+            "04d_asessment-benchmarks.qmd",
+            "04e_assessment-projections.qmd",
+            "05_discussion.qmd",
+            "06_acknowledgments.qmd",
+            "07_references.qmd",
+            "08_tables.qmd",
+            "09_figures.qmd",
+            "10_notes.qmd",
+            "11_appendix.qmd"
           ),
           label = c(
-            "executive_summary",
-            "introduction",
-            "data",
-            "modeling_approach",
-            "results",
-            "projections",
-            "discussion",
-            "acknowlesgements",
-            "references",
-            "tables",
-            "figures",
-            "appendix"
+            "01_executive_summary",
+            "02_introduction",
+            "03_data",
+            "04a_assessment-configuration",
+            "04b_assessment-results",
+            "04c_assessment-sensitivity",
+            "04d_asessment-benchmarks",
+            "04e_assessment-projections",
+            "05_discussion",
+            "06_acknowledgments",
+            "07_references",
+            "08_tables",
+            "09_figures",
+            "10_notes",
+            "11_appendix"
           )
         )
       } else {
@@ -611,18 +618,21 @@ create_template <- function(
 
           if (is.null(custom_sections)) {
             sec_list1 <- list(
-              "executive_summary.qmd",
-              "introduction.qmd",
-              "data.qmd",
-              "modeling_approach.qmd",
-              "results.qmd",
-              "projections.qmd",
-              "discussion.qmd",
-              "acknowledgments.qmd",
-              "references.qmd",
-              "tables.qmd",
-              "figures.qmd",
-              "appendix.qmd"
+              "01_executive_summary.qmd",
+              "02_introduction.qmd",
+              "03_data.qmd",
+              "04a_assessment-configuration.qmd",
+              "04b_assessment-results.qmd",
+              "04c_assessment-sensitivity.qmd",
+              "04d_asessment-benchmarks.qmd",
+              "04e_assessment-projections.qmd",
+              "05_discussion.qmd",
+              "06_acknowledgments.qmd",
+              "07_references.qmd",
+              "08_tables.qmd",
+              "09_figures.qmd",
+              "10_notes.qmd",
+              "11_appendix.qmd"
             )
             sec_list2 <- add_section(
               new_section = new_section,
@@ -645,10 +655,10 @@ create_template <- function(
               stop("Defined customizations do not match one or all of the relative placement of a new section. Please review inputs.")
             }
             if (include_tables) {
-              sec_list1 <- c(sec_list1, "tables.qmd")
+              sec_list1 <- c(sec_list1, "08_tables.qmd")
             }
             if (include_figures) {
-              sec_list1 <- c(sec_list1, "figures.qmd")
+              sec_list1 <- c(sec_list1, "09_figures.qmd")
             }
             sec_list2 <- add_section(
               new_section = new_section,
@@ -736,32 +746,38 @@ create_template <- function(
       if (custom == FALSE) {
         sections <- add_child(
           c(
-            "executive_summary.qmd",
-            "introduction.qmd",
-            "data.qmd",
-            "modeling_approach.qmd",
-            "results.qmd",
-            "projections.qmd",
-            "discussion.qmd",
-            "acknowledgments.qmd",
-            "references.qmd",
-            "tables.qmd",
-            "figures.qmd",
-            "appendix.qmd"
+            "01_executive_summary.qmd",
+            "02_introduction.qmd",
+            "03_data.qmd",
+            "04a_assessment-configuration.qmd",
+            "04b_assessment-results.qmd",
+            "04c_assessment-sensitivity.qmd",
+            "04d_asessment-benchmarks.qmd",
+            "04e_assessment-projections.qmd",
+            "05_discussion.qmd",
+            "06_acknowledgments.qmd",
+            "07_references.qmd",
+            "08_tables.qmd",
+            "09_figures.qmd",
+            "10_notes.qmd",
+            "11_appendix.qmd"
           ),
           label = c(
-            "executive_summary",
-            "introduction",
-            "data",
-            "modeling_approach",
-            "results",
-            "projections",
-            "discussion",
-            "acknowlesgements",
-            "references",
-            "tables",
-            "figures",
-            "appendix"
+            "01_executive_summary",
+            "02_introduction",
+            "03_data",
+            "04a_assessment-configuration",
+            "04b_assessment-results",
+            "04c_assessment-sensitivity",
+            "04d_asessment-benchmarks",
+            "04e_assessment-projections",
+            "05_discussion",
+            "06_acknowledgments",
+            "07_references",
+            "08_tables",
+            "09_figures",
+            "10_notes",
+            "11_appendix"
           )
         )
       } else {
@@ -778,22 +794,25 @@ create_template <- function(
 
           if (is.null(custom_sections)) {
             sec_list1 <- list(
-              "executive_summary.qmd",
-              "introduction.qmd",
-              "data.qmd",
-              "modeling_approach.qmd",
-              "results.qmd",
-              "projections.qmd",
-              "discussion.qmd",
-              "acknowledgments.qmd",
-              "references.qmd",
-              "tables.qmd",
-              "figures.qmd",
-              "appendix.qmd"
+              "01_executive_summary.qmd",
+              "02_introduction.qmd",
+              "03_data.qmd",
+              "04a_assessment-configuration.qmd",
+              "04b_assessment-results.qmd",
+              "04c_assessment-sensitivity.qmd",
+              "04d_asessment-benchmarks.qmd",
+              "04e_assessment-projections.qmd",
+              "05_discussion.qmd",
+              "06_acknowledgments.qmd",
+              "07_references.qmd",
+              "08_tables.qmd",
+              "09_figures.qmd",
+              "10_notes.qmd",
+              "11_appendix.qmd"
             )
             sec_list2 <- add_section(
               new_section = new_section,
-              new_section = section_location,
+              section_location = section_location,
               custom_sections = sec_list1,
               subdir = subdir
             )
@@ -808,7 +827,7 @@ create_template <- function(
             # Create new sections as .qmd in folder
             sec_list2 <- add_section(
               new_section = new_section,
-              new_section = section_location,
+              section_location = section_location,
               custom_sections = sec_list1,
               subdir = subdir
             )
diff --git a/R/utils.R b/R/utils.R
index 610e7995..944400e4 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -2,31 +2,6 @@
 ####    Utilities    ####
 #########################
 
-#---- add_base_section ----
-
-#' Add selected sections to outline
-#'
-#' @param x inherited 'custom_sections' parameter from create_template
-#'
-#' @return Call and copy the sections in the package templates to create an outline for a stock assessment
-#' @noRd
-#'
-#' @examples add_base_section(c("abstract", "model", "results"))
-add_base_section <- function(x) {
-  sec_sel <- gsub(" ", "_", tolower(gsub("(.)([A-Z])", "\\1 \\2", x)))
-  section_list <- list()
-  for (i in 1:length(sec_sel)) {
-    sec_file <- grep(
-      x = list.files(system.file("templates", "skeleton", package = "asar")),
-      pattern = sec_sel[i],
-      value = TRUE
-    )
-    if (identical(sec_file, character(0))) stop("One or more section name(s) does not exist. Please check the spelling or if you are tring to add a section that is not in the default template, please use parameter 'custom_sections' and refer to documentation. To check which sections are in the base template please run list.files(system.file('templates', 'skeleton', package = 'ASAR')) in your console")
-    sec_file -> section_list[i]
-  }
-  section_list
-}
-
 #---- get_ncol ----
 # Helper for SS3 output converter
 # Sourced from r4ss
diff --git a/inst/templates/skeleton/01_executive_summary.qmd b/inst/templates/skeleton/01_executive_summary.qmd
new file mode 100644
index 00000000..d9ee0f7a
--- /dev/null
+++ b/inst/templates/skeleton/01_executive_summary.qmd
@@ -0,0 +1,12 @@
+## Executive Summary
+
+<!--- Where possible, the executive summary should paraphrase the shared content of the body of the report to minimize redundancy.--->
+
+### Assessment Model
+
+<!-- Include a short statement describing the assessment model used for the current management cycle and any data updates. -->
+
+### Reference Points, Stock Status, and Projections
+
+<!-- Short summary of reference points, stock status, and projections. When using `asar`, tables of reference points and projections will be automatically generated. -->
+
diff --git a/inst/templates/skeleton/02_introduction.qmd b/inst/templates/skeleton/02_introduction.qmd
new file mode 100644
index 00000000..50ef8274
--- /dev/null
+++ b/inst/templates/skeleton/02_introduction.qmd
@@ -0,0 +1,25 @@
+## Introduction
+
+Testing adding in an introduction for `r params$species`. There is currently no read of parameters for child documents.
+
+<!-- The intent is to keep this section to 2-3 pages and provide a high-level summary of the assessment findings. The intention is to provide enough information in this section so the audience does not need to reference previous documents. Please include the species scientific name at the first mention of its common name. -->
+
+
+### Management History
+
+<!---
+Briefly describe the management history of the stock and status. Please only touch on historical policies that would have impacted modeling decisions or would be critical knowledge about the species that might affect its population dynamics.
+--->
+
+### Fishery Descriptions
+
+<!---
+Short summary of fleet composition (i.e., boat types), gear types, species targeted, and fishing grounds (one paragraph).
+--->
+
+### Ecosystem Considerations
+
+<!---
+If this section is not relevant, please ignore. However, the default will state, “Ecosystem considerations and/or climate indicators were not included in this assessment.”
+--->
+
diff --git a/inst/templates/skeleton/03_data.qmd b/inst/templates/skeleton/03_data.qmd
new file mode 100644
index 00000000..2881d805
--- /dev/null
+++ b/inst/templates/skeleton/03_data.qmd
@@ -0,0 +1,31 @@
+## Data
+
+<!--- Provide temporal and spatial resolutions or sample size where appropriate for each of the subsections, below.--->
+
+### Stock ID
+
+<!-- Provide a detailed description of the stock, if appropriate, as well as quantitative studies or data behind the decision-making process. -->
+
+### Life History
+
+<!-- Describe the stock's growth, maturity, fecundity, natural mortality, meristics, etc. -->
+
+### Landings
+
+<!-- Describe the retained catch and discards. -->
+
+### Indices and Standardization
+
+<!-- Describe both the fishery dependent and independent data. -->
+
+### Composition Data
+
+<!-- Describe composition data related to age and length, including  aging error and reweighting. -->
+
+### Absolute Abundance
+
+<!-- Describe absolute abundance, if applicable. -->
+
+### Environmental/Ecosystem Indicator Data
+
+<!-- Describe the environmental/ecosystem indicator data. If none are considered, include a blanket statement. -->
diff --git a/inst/templates/skeleton/04a_assessment-configuration.qmd b/inst/templates/skeleton/04a_assessment-configuration.qmd
new file mode 100644
index 00000000..e865ae17
--- /dev/null
+++ b/inst/templates/skeleton/04a_assessment-configuration.qmd
@@ -0,0 +1,11 @@
+## Assessment
+
+### Current Modeling Approach
+
+<!--- Include a short, general overview of the modeling platform, including the reference to the model paper or online reference. If using `asar`, a portion of this will be generated based on the stated model. Please include a short description of changes between the approach from the last assessment cycle to the current. --->
+
+### Configuration of the Base Model
+
+<!--- Describe the setup of the stock assessment model. --->
+
+
diff --git a/inst/templates/skeleton/04b_assessment-results.qmd b/inst/templates/skeleton/04b_assessment-results.qmd
new file mode 100644
index 00000000..55dee7fd
--- /dev/null
+++ b/inst/templates/skeleton/04b_assessment-results.qmd
@@ -0,0 +1,14 @@
+### Modeling Results
+
+<!-- For each of the following subsections, please describe the results for the base model. -->
+
+#### Parameter Estimates
+
+
+#### Recruitment Estimates and Deviations
+
+
+#### Model Fits
+
+
+#### Model Diagnostics
diff --git a/inst/templates/skeleton/04c_assessment-sensitivity.qmd b/inst/templates/skeleton/04c_assessment-sensitivity.qmd
new file mode 100644
index 00000000..a3549592
--- /dev/null
+++ b/inst/templates/skeleton/04c_assessment-sensitivity.qmd
@@ -0,0 +1 @@
+### Sensitivity Analyses
diff --git a/inst/templates/skeleton/04d_assessment-benchmarks.qmd b/inst/templates/skeleton/04d_assessment-benchmarks.qmd
new file mode 100644
index 00000000..816a6e59
--- /dev/null
+++ b/inst/templates/skeleton/04d_assessment-benchmarks.qmd
@@ -0,0 +1,3 @@
+### Management Benchmarks
+
+<!-- Decisions on management metrics/benchmarks (e.g., provide a rationale for why a specific F-proxy was recommended for management). -->
diff --git a/inst/templates/skeleton/04e_assessment-projections.qmd b/inst/templates/skeleton/04e_assessment-projections.qmd
new file mode 100644
index 00000000..7c06e550
--- /dev/null
+++ b/inst/templates/skeleton/04e_assessment-projections.qmd
@@ -0,0 +1,3 @@
+### Projections
+
+<!--- Descriptions of stock status, biological reference points (BRPs), trends, and rebuilding times for each scenario. --->
diff --git a/inst/templates/skeleton/05_discussion.qmd b/inst/templates/skeleton/05_discussion.qmd
new file mode 100644
index 00000000..c342da89
--- /dev/null
+++ b/inst/templates/skeleton/05_discussion.qmd
@@ -0,0 +1,3 @@
+## Discussion
+
+<!--- The discussion is dependent on analyst/assessment/region. Include subsections discussing ecosystem considerations (if applicable) and research recommendations/improvements to the assessment. --->
diff --git a/inst/templates/skeleton/acknowledgments.qmd b/inst/templates/skeleton/06_acknowledgments.qmd
similarity index 100%
rename from inst/templates/skeleton/acknowledgments.qmd
rename to inst/templates/skeleton/06_acknowledgments.qmd
diff --git a/inst/templates/skeleton/references.qmd b/inst/templates/skeleton/07_references.qmd
similarity index 100%
rename from inst/templates/skeleton/references.qmd
rename to inst/templates/skeleton/07_references.qmd
diff --git a/inst/templates/skeleton/10_notes.qmd b/inst/templates/skeleton/10_notes.qmd
new file mode 100644
index 00000000..9c179a38
--- /dev/null
+++ b/inst/templates/skeleton/10_notes.qmd
@@ -0,0 +1,3 @@
+## Notes
+
+<!-- Short statement on internal reference to the report (e.g., SEDAR 99, SAFE, management track). -->
diff --git a/inst/templates/skeleton/appendix.qmd b/inst/templates/skeleton/11_appendix.qmd
similarity index 100%
rename from inst/templates/skeleton/appendix.qmd
rename to inst/templates/skeleton/11_appendix.qmd
diff --git a/inst/templates/skeleton/assessment_glossaries.tex b/inst/templates/skeleton/assessment_glossaries.tex
deleted file mode 100644
index 389f2933..00000000
--- a/inst/templates/skeleton/assessment_glossaries.tex
+++ /dev/null
@@ -1,278 +0,0 @@
-% Glossary from sa4ss - NW and SW FSC
-\newacronym{abc}{ABC}{Acceptable Biological Catch}
-\newacronym{ace}{ACE}{Army Corp of Engineers}
-\newacronym{acl}{ACL}{annual catch limit}
-\newacronym{act}{ACT}{annual catch target}
-\newacronym{adfg}{ADF\&G}{Alaska Department of Fish and Game}
-\newacronym{admb}{ADMB}{AD Model Builder}
-\newacronym{afa}{AFA}{American Fisheries Act}
-\newacronym{afsc}{AFSC}{Alaska Fisheries Science Center}
-\newacronym{aic}{AIC}{Akaike information criterion}
-\newacronym{ais}{AIS}{Automatic Identification System}
-\newacronym{akfin}{AKFIN}{Alaska Fisheries Information Network}
-\newacronym{akro}{AKRO}{Alaska Regional Office}
-\newacronym{am}{AM}{accountability measures}
-\newacronym{apecs}{APECS}{Assessment Profile, Ecosystem Considerations, and Socioeconomics}
-\newacronym{ashop}{ASHOP}{At-Sea Hake Observer Program}
-\newacronym{asmfc}{ASMFC}{Atlantic States Marine Fisheries Commission}
-\newacronym{bac}{BAC}{Block Area Closure}
-\newacronym{bcca}{BCCA}{Bottom Contact Closed Area}
-\newacronym{bcigfp}{Integrated Program}{British Columbia Integrated Groundfish Program}
-\newacronym{bic}{BIC}{Bayesian information criterion}
-\newacronym{bo}{BO}{Biological Opinion}
-\newacronym{brd}{BRD}{bycatch reduction device}
-\newacronym{bsai}{BS\slash AI}{Bering Sea\slash Aleutian Islands}
-\newacronym{bsia}{BSIA}{best scientific information available}
-\newacronym{btca}{BTCA}{Bottom Trawl Closed Area}
-\newacronym{cands}{C\&S}{ceremonial and subsistence}
-\newacronym{caal}{CAAL}{conditional age-at-length}
-\newacronym{calcofi}{CalCOFI}{California Cooperative Oceanic Fisheries Investigations}
-\newacronym{calpoly}{Cal Poly}{California Polytechnic State University}
-\newacronym{cbnms}{CBNMS}{Cordell Bank National Marine Sanctuary}
-\newacronym{calcom}{CalCOM}{CalCOM database for the California Cooperative Survey}
-\newacronym{cca}{CCA}{Cowcod Conservation Area}
-\newacronym{cce}{CCE}{California Current Ecosystem}
-\newacronym{cdfw}{CDFW}{California Department of Fish and Wildlife}
-\newacronym{cesu}{CESU}{Cooperative Ecosystem Studies Unit}
-\newacronym{cinms}{CINMS}{Channel Islands National Marine Sanctuary}
-\newacronym{cfmc}{CFMC}{Caribbean Fisheries Management Council}
-\newacronym{cfr}{CFR}{Code of Federal Regulations}
-\newacronym{ci}{CI}{Cooperative Institute}
-\newacronym{cie}{CIE}{Center for Independent Experts}
-\newacronym{cmsp}{CMSP}{Coastal and Marine Spatial Planning}
-\newacronym{copc}{\href{http://www.opc.ca.gov/}{COPC}}{\href{http://www.opc.ca.gov/}{California Ocean Protection Council}}
-\newacronym{covid}{COVID-19}{Coronavirus disease}
-\newacronym{cp}{CP}{catcher-processor}
-\newacronym{cpfv}{CPFV}{commercial passenger fishing vessel}
-\newacronym{cps}{CPS}{coastal pelagic species}
-\newacronym{cpue}{CPUE}{catch per unit effort}
-\newacronym{crca}{CRCA}{California Rockfish Conservation Area}
-\newacronym{crfs}{CRFS}{California Recreational Fisheries Survey}
-\newacronym{csmp}{CSMP}{California Seafloor Mapping Program}
-\newacronym{csp}{CSP}{Halibut Catch Sharing Plan}
-\newacronym{csumb}{\href{http://seafloor.otterlabs.org/}{CSUMB}}{\href{http://seafloor.otterlabs.org/}{California State University at Monterey Bay Seafloor Mapping Lab}}
-\newacronym{cv}{CV}{catcher vessel}
-\newacronym{cwa}{CWA}{Clean Water Act}
-\newacronym{czma}{CZMA}{Coastal Zone Management Act}
-\newacronym{di}{D\&I}{Diversity and Inclusion}
-\newacronym{dah}{DAH}{domestic annual harvest}
-\newacronym{dap}{DAP}{domestic annual processing}
-\newacronym{dfo}{DFO}{Fisheries and Oceans Canada}
-\newacronym{doc}{DOC}{Department of Commerce}
-\newacronym{doi}{DOI}{Department of Interior}
-\newacronym{dscs}{DSCD}{deep sea coral and sponge}
-\newacronym{dtl}{DTL}{daily trip limit}
-\newacronym{dts}{DTS}{dover sole, thornyhead, and trawl-caught sablefish complex}
-\newacronym{dw}{DW}{disk width}
-\newacronym{eas}{EAS}{Ecosystem Advisory Subpanel}
-\newacronym{ebm}{EBM}{ecosystem-based management}
-\newacronym{ebfm}{EBFM}{ecosystem-based fisheries management}
-\newacronym{ebs}{EBS}{Eastern Bering Sea}
-\newacronym{ec}{EC}{ecosystem component}
-\newacronym{eeop}{EEOP}{Equal Employment Opportunity Plan}
-\newacronym{eez}{EEZ}{exclusive economic zone}
-\newacronym{efh}{EFH}{essential fish habitat}
-\newacronym{efhca}{EFHCA}{essential fish habitat conservation area}
-\newacronym{efin}{EFIN}{Economic Fishery Information Network}
-\newacronym{efp}{EFP}{exempted fishing permit}
-\newacronym{eis}{EIS}{Environmental Impact Statement}
-\newacronym{eli}{ELI}{Ecosystem Linkage Index}
-\newacronym{em}{EM}{electronic monitoring}
-\newacronym{emer}{EM\slash ER}{Electronic Monitoring\slash Electronic Reporting}
-\newacronym{enso}{ENSO}{El Ni{\~n}o Southern Oscillation}
-\newacronym{epp}{EPP}{Educational Partnership Program}
-\newacronym{esa}{ESA}{Endangered Species Act}
-\newacronym{esu}{ESU}{evolutionary significant unit}
-\newacronym{fep}{FEP}{Fishery Ecosystem Plan}
-\newacronym{fis}{FIS}{Fisheries Information System}
-\newacronym{fl}{FL}{fork length}
-\newacronym{fmp}{FMP}{Fishery Management Plan}
-\newacronym{fmsy}{$F_{MSY}$}{fishing mortality at maximum sustainable yield}
-\newacronym{fmu}{FMU}{Fishery Management Unit}
-\newacronym{foia}{FOIA}{Freedom of Information Act}
-\newacronym{fram}{FRAM}{Fishery Resource and Monitoring Division}
-\newacronym{fssi}{FSSI}{Fish Stock Sustainability Index}
-\newacronym{fws}{FWS}{U.S. Fish and Wildlife Service}
-\newacronym{gap}{GAP}{Groundfish Advisory Subpanel}
-\newacronym{garfo}{GARFO}{Greater Atlantic Regional Fisheries Office}
-\newacronym{gca}{GCA}{Groundfish Conservation Area}
-\newacronym{gdp}{GDP}{gross domestic product}
-\newacronym{gemm}{GEMM}{Groundfish Expanded Mortality Multi-Year}
-\newacronym{gfa}{GFA}{groundfish fishing area}
-\newacronym{gfnms}{GFNMS}{Gulf of the Farallones National Marine Sanctuary}
-\newacronym{gis}{GIS}{Geographic Information System}
-\newacronym{glm}{GLM}{Generalized Linear Model}
-\newacronym{gmfmc}{GMFMC}{Gulf of Mexico Fishery Management Council}
-\newacronym{gmt}{GMT}{Groundfish Management Team}
-\newacronym{goa}{GOA}{Gulf of Alaska}
-\newacronym{gps}{GPS}{Global Positioning System}
-\newacronym{gsmfc}{GSMFC}{Gulf States Marine Fisheries Commission}
-\newacronym{haip}{HAIP}{Habitat Assessment Improvement Plan}
-\newacronym{hapc}{HAPC}{Habitat Area of Particular Concern}
-\newacronym{hcr}{HCR}{harvest control rule}
-\newacronym{hg}{HG}{harvest guideline}
-\newacronym{hms}{HMS}{highly migratory species}
-\newacronym{hsp}{HSP}{habitat suitability probability}
-\newacronym{hud}{HUD}{Habitat Use Database}
-\newacronym{iattc}{IATTC}{Inter-American Tropical Tuna Commission}
-\newacronym{ibq}{IBQ}{individual bycatch quota}
-\newacronym{idfg}{IDFG}{Idaho Department of Fish and Game}
-\newacronym{iea}{IEA}{Integrated Ecosystem Assessment}
-\newacronym{ifq}{IFQ}{individual fishing quota}
-\newacronym{inpfc}{INPFC}{International North Pacific Fishery Commission}
-\newacronym{iphc}{IPHC}{International Pacific Halibut Commission}
-\newacronym{iq}{IQ}{individual quota}
-\newacronym{isw}{ISW}{interspiracular width}
-\newacronym{itq}{ITQ}{individual transferable or tradeable quota}
-\newacronym{iuu}{IUU}{illegal, unregulated, and unreported}
-\newacronym{jv}{JV}{joint-venture}
-\newacronym{jvp}{JVP}{joint-venture processing}
-\newacronym{lapp}{LAPP}{Limited Access Privilege Program}
-\newacronym{le}{LE}{limited entry}
-\newacronym{lmrcsc}{LMRCSC}{Living Marine Resources Cooperative Science Center}
-\newacronym{mafmc}{MAFMC}{Mid-Atlantic Fishery Management Council}
-\newacronym{marmap}{MARMAP}{Marine Resource Monitoring and Assessment Program}
-\newacronym{marpol}{MARPOL}{International Convention for the Prevention of Pollution from Ships}
-\newacronym{mbnms}{MBNMS}{Monterey Bay National Marine Sanctuary}
-\newacronym{mbta}{MBTA}{Migratory Bird Treaty Act}
-\newacronym{mfmt}{MFMT}{maximum fishing mortality threshold}
-\newacronym{mlr}{MLR}{minimum landing requirement}
-\newacronym{mle}{MLE}{maximum likelihood estimation}
-\newacronym{mlml}{\href{https://www.mlml.calstate.edu/}{MLML}}{\href{https://www.mlml.calstate.edu/}{Moss Landing Marine Laboratories}}
-\newacronym{mlpa}{MLPA}{California Marine Life Protection Act}
-\newacronym{mmpa}{MMPA}{Marine Mammal Protection Act}
-\newacronym{moa}{MOA}{Memorandum of Agreement}
-\newacronym{mou}{MOU}{Memorandum of Understanding}
-\newacronym{mpa}{MPA}{Marine Protected Area}
-\newacronym{mrfss}{MRFSS}{Marine Recreational Fisheries Statistics Survey}
-\newacronym{mrep}{MREP}{Marine Resource Education Program}
-\newacronym{mrip}{MRIP}{Marine Recreation Information Program}
-\newacronym{ms}{MS}{mothership}
-\newacronym{mse}{MSE}{management strategy evaluation}
-\newacronym{msfcma}{MSFCMA}{Magnuson-Stevens Fishery Conservation and Management Act}
-\newacronym{msi}{MSI}{Minority Serving Institution}
-\newacronym{msra}{MSRA}{Magnuson-Stevens Fishery Conservation and Management Reauthorization Act of 2006}
-\newacronym{msst}{MSST}{minimum stock size threshold}
-\newacronym{msy}{\emph{MSY}}{maximum sustainable yield}
-\newacronym{n-fish}{N-FISH}{National Marine Fisheries Service Diversity Intern Program}
-\newacronym{na}{NA}{not available}
-\newacronym{namss}{\href{https://walrus.wr.usgs.gov/namss/}{NAMSS}}{\href{https://walrus.wr.usgs.gov/namss/}{United States Geological Survey National Archive of Marine Seismic Surveys}}
-\newacronym{ncss}{NCSS}{National Climate Science Strategy}
-\newacronym{neamap}{NEAMAP}{Northeast Area Monitoring and Assessment Program}
-\newacronym{nefmc}{NEFMC}{New England Fishery Management Council}
-\newacronym{nefsc}{NEFSC}{Northeast Fisheries Science Center}
-\newacronym{nepa}{NEPA}{National Environmental Policy Act}
-\newacronym{ngsa}{NGSA}{Next Generation Stock Assessment}
-\newacronym{nm}{nm}{nautical mile}
-\newacronym{nmfs}{NMFS}{National Marine Fisheries Service}
-\newacronym{nms}{NMS}{National Marine Sanctuary}
-\newacronym{nmsa}{NMSA}{National Marine Sanctuaries Act}
-\newacronym{noaa}{\href{https://www.noaa.gov/}{NOAA}}{\href{https://www.noaa.gov/}{National Oceanic \& Atmospheric Administration}}
-\newacronym{noaagc}{NOAA GC}{National Oceanic \& Atmospheric Administration General Counsel}
-\newacronym{noi}{NOI}{notice of intent}
-\newacronym{norpac}{NORPAC}{North Pacific Database Program}
-\newacronym{nos}{NOS}{National Ocean Service}
-\newacronym{npfmc}{NPFMC}{North Pacific Fishery Management Council}
-\newacronym{npoa}{NPOA}{National Plan of Action}
-\newacronym{nrc}{NRC}{National Research Council}
-\newacronym{nrcc}{NRCC}{Northeast Regional Coordinating Council}
-\newacronym{nrdc}{NRDC}{Natural Resources Defense Council}
-\newacronym{ns1}{NS1}{National Standard 1}
-\newacronym{nsf}{NSF}{National Science Foundation}
-\newacronym{nsg}{NSG}{National Standards guidelines}
-\newacronym{nwfsc}{NWFSC}{Northwest Fisheries Science Center}
-\newacronym{nwifc}{NWIFC}{Northwest Indian Fisheries Commission}
-\newacronym{nwr}{NWR}{Northwest Region}
-\newacronym{oa}{OA}{open access}
-\newacronym{oaq}{OAQ}{Office of Aquaculture}
-\newacronym{ocnms}{OCNMS}{Olympic Coast National Marine Sanctuary}
-\newacronym{odfw}{ODFW}{Oregon Department of Fish and Wildlife}
-\newacronym{ofl}{OFL}{overfishing limit}
-\newacronym{opm}{OPM}{Office of Personnel  Management}
-\newacronym{orbs}{ORBS}{Oregon Department of Fish and Wildlife Oregon Recreational Boat Survey}
-\newacronym{osp}{OSP}{Washington Department of Fish and Wildlife Ocean Sampling Program}
-\newacronym{oy}{OY}{optimum yield}
-\newacronym{pacfin}{PacFIN}{Pacific Fisheries Information Network}
-\newacronym{pbr}{PBR}{Potential Biological Removal}
-\newacronym{pcffa}{PCFFA}{Pacific Coast Federation of Fishermen's Associations}
-\newacronym{pcmsc}{\href{https://www.usgs.gov/centers/pcmsc}{PCMSC}}{\href{https://www.usgs.gov/centers/pcmsc}{Pacific Coastal and Marine Science Center}}
-\newacronym{pdf}{PDF}{probability density function}
-\newacronym{pdo}{PDO}{Pacific Decadal Oscillation}
-\newacronym{pep}{PEP}{Woods Hole Partnership Education Program}
-\newacronym{pfmc}{PFMC}{Pacific Fishery Management Council}
-\newacronym{pifsc}{PIFSC}{Pacific Islands Fisheries Science Center}
-\newacronym{piro}{PIRO}{Pacific Islands Regional Office}
-\newacronym{pnw}{PNW}{Pacific Northwest}
-\newacronym{pra}{PRA}{Paperwork Reduction Act}
-\newacronym{prsaip}{PRSAIP}{Protected Resources Stock Assessment Improvement Plan}
-\newacronym{psmfc}{PSMFC}{Pacific States Marine Fisheries Commission}
-\newacronym{qaqc}{QA\slash QC}{Quality Assurance\slash Quality Control}
-\newacronym{qp}{QP}{quota pounds}
-\newacronym{qs}{QS}{quota shares}
-\newacronym{quest}{QUEST}{Quantitative Ecology and Socioeconomics Training Program}
-\newacronym{raq}{RAQ}{Regional Aquaculture Coordinator}
-\newacronym{rca}{RCA}{Rockfish Conservation Area}
-\newacronym{recfin}{RecFIN}{Recreational Fishery Information Network}
-\newacronym{rer}{RER}{Recovery Exploitation Rate}
-\newacronym{rfmo}{RFMO}{Regional Fishery Management Organization}
-\newacronym{rir}{RIR}{Regulatory Impact Review}
-\newacronym{rov}{ROV}{remote operated vehicle}
-\newacronym{rtr}{RTR}{Research Training and Recruitment}
-\newacronym{s-aslope}{Slope Survey}{Alaska Fisheries Science Center Slope Survey}
-\newacronym{s-ccfrp}{\href{https://www.mlml.calstate.edu/ccfrp/}{CCFRP}}{\href{https://www.mlml.calstate.edu/ccfrp/}{California Collaborative Fisheries Research Program}}
-\newacronym{s-nshelf}{NWFSC Shelf Survey}{Northwest Fisheries Science Center Shelf Survey}
-\newacronym{s-nslope}{NWFSC Slope Survey}{Northwest Fisheries Science Center Slope Survey}
-\newacronym{s-tri}{Triennial Survey}{Alaska Fisheries Science Center/Northwest Fisheries Science Center West Coast Triennial Shelf Survey}
-\newacronym{s-wcgbt}{WCGBTS}{Northwest Fisheries Science Center West Coast Groundfish Bottom Trawl Survey}
-\newacronym{s-hkl}{Hook and Line Survey}{Northwest Fisheries Science Center Hook and Line Survey}
-\newacronym{safe}{SAFE}{Stock Assessment and Fishery Evaluation}
-\newacronym{safmc}{SAFMC}{South Atlantic Fishery Management Council}
-\newacronym{saip}{SAIP}{Stock Assessment Improvement Plan}
-\newacronym{sam}{SAM}{State-Space Assessment Model}
-\newacronym{sawsarc}{SAW\slash SARC}{Stock Assessment Workshop\slash Stock Assessment Review Committee}
-\newacronym{sb}{SB}{spawning biomass}
-\newacronym{ssb}{SB}{spawning biomass}
-\newacronym{scaa}{SCAA}{Statistical Catch-at-Age Assessment}
-\newacronym{sdc}{SDC}{status determination criteria}
-\newacronym{sdmtmb}{\texttt{sdmTMB}}{\href{https://github.com/pbs-assess/sdmtmb}{Species Distribution Models with Template Model Builder}}
-\newacronym{sebs}{SEBS}{Shore and Estuary Boat Survey, Oregon Department of Fish and Wildlife}
-\newacronym{sec}{Secretary}{United States Secretary of Commerce}
-\newacronym{sedar}{SEDAR}{Southeast Data, Assessment, and Review}
-\newacronym{sefis}{SEFIS}{Southeast Fishery Independent Survey}
-\newacronym{sefsc}{SEFSC}{Southeast Fisheries Science Center}
-\newacronym{sero}{SERO}{Southeast Regional Office}
-\newacronym{sfa}{SFA}{Sustainable Fisheries Act of 1996}
-\newacronym{ses}{SES}{social--ecological system}
-\newacronym{sia}{SIA}{Social Impact Analysis}
-\newacronym{spr}{SPR}{spawning potential ratio}
-\newacronym{ssc}{SSC}{Scientific and Statistical Committee}
-\newacronym{sst}{SST}{sea-surface temperature}
-\newacronym{star}{STAR}{Stock Assessment Review}
-\newacronym{ss3}{SS3}{Stock Synthesis}
-\newacronym{swfsc}{SWFSC}{Southwest Fisheries Science Center}
-\newacronym{tac}{TAC}{total allowable catch}
-\newacronym{tl}{TL}{total length}
-\newacronym{tmb}{\href{https://kaskr.github.io/adcomp/index.html}{TMB}}{\href{https://kaskr.github.io/adcomp/index.html}{Template Model Builder}}
-\newacronym{tnc}{TNC}{The Nature Conservancy}
-\newacronym{tor}{ToR}{Terms of Reference}
-\newacronym{ua}{U\&A}{usual and accustomed}
-\newacronym{unols}{UNOLS}{University-National Oceanographic Laboratory System}
-\newacronym{uscg}{USCG}{United States Coast Guard}
-\newacronym{usfs}{USFS}{United States Forest Service}
-\newacronym{usfws}{USFWS}{United States Fish and Wildlife Service}
-\newacronym{usgs}{USGS}{United States Geological Survey}
-\newacronym{vms}{VMS}{Vessel Monitoring System}
-\newacronym{vast}{VAST}{vector autoregressive spatio-temporal}
-\newacronym{wcgop}{WCGOP}{West Coast Groundfish Observer Program}
-\newacronym{wcpfc}{WCPFC}{Western and Central Pacific Fisheries Commission}
-\newacronym{wcr}{WCR}{West Coast Region}
-\newacronym{wcspa}{WCSPA}{West Coast Seafood Processors Association}
-\newacronym{wcvi}{WCVI}{West Coast Vancouver Island}
-\newacronym{wdfw}{WDFW}{Washington Department of Fish and Wildlife}
-\newacronym{wfmo}{WFMO}{Workforce Management Office}
-\newacronym{wfoa}{WFOA}{Western Fishboat Owners Association}
-\newacronym{wpfmc}{WPFMC}{Western Pacific Fishery Management Council}
-\newacronym{wpsar}{WPSAR}{Western Pacific Stock Assessment Review}
-\newacronym{yrca}{YRCA}{Yelloweye Rockfish Conservation Area}
-\newacronym{yoy}{YOY}{young of the year}
-
diff --git a/inst/templates/skeleton/data.qmd b/inst/templates/skeleton/data.qmd
deleted file mode 100644
index 208bd248..00000000
--- a/inst/templates/skeleton/data.qmd
+++ /dev/null
@@ -1,14 +0,0 @@
-## Data {#sec-data}
-
-<!---
-Include the following:
-- Temporal and spatial resolutions and number of samples
-- Stock ID (more detailed description if appropriate and qualitative studies or data are behind the decision making)
-- Life history (growth, maturity, fecundity, natural mortality, meristics, ect.)
-- Landings (retained catch and discards)
-- Indices and standardization (fishery dependent and independent)
-- Composition data - age, length (Description, ageing error, reweighting)
-- Absolute abundance (if applicable)
-- Environmental/ecosystem indicator data
-- Reweighting or effective sample size adjustments
---->
diff --git a/inst/templates/skeleton/discussion.qmd b/inst/templates/skeleton/discussion.qmd
deleted file mode 100644
index d10684ab..00000000
--- a/inst/templates/skeleton/discussion.qmd
+++ /dev/null
@@ -1,5 +0,0 @@
-## Discussion {#sec-discussion}
-
-<!---
-There are no specified guidelines to structure this section; however, please include subsections discussing ecosystem considerations (if applicable) and research recommendations/improvements to the assessment.
---->
diff --git a/inst/templates/skeleton/executive_summary.qmd b/inst/templates/skeleton/executive_summary.qmd
deleted file mode 100644
index f6cd6695..00000000
--- a/inst/templates/skeleton/executive_summary.qmd
+++ /dev/null
@@ -1,24 +0,0 @@
-## Executive Summary {#sec-executive-summary}
-
-<!---
-Table of updates among the current stock assessment report
---->
-
-### Assessment Methods {#sec-assessment-methods}
-
-<!---
-- Current Assessment
-- Additional data updates
-- Major changes
---->
-
-### Stock Status {#sec-stock-status}
-
-<!---
-Short description followed by a tables with reference points, stock status, and projections
-
-If applicable, please add the stock TOR and responses here.
---->
-
-
-
diff --git a/inst/templates/skeleton/introduction.qmd b/inst/templates/skeleton/introduction.qmd
deleted file mode 100644
index aa9f28ac..00000000
--- a/inst/templates/skeleton/introduction.qmd
+++ /dev/null
@@ -1,29 +0,0 @@
-## Introduction {#sec-introduction}
-
-Testing adding in an introduction for `r params$species`. There is currently no read of parameters for child documents.
-
-### Management and Assessment History {#sec-history}
-
-<!---
-- Provide a brief description of management history of the stock and status (including change in fishery behavior).
-- History of assessment approaches.
---->
-
-### Stock Structure and ID {#sec-stock-id}
-
-<!---
-Provide a short description (a longer explanation will be included in the data section if applicable)
---->
-
-### Fishery Descriptions {#sec-fishery-desscriptions}
-
-<!---
-Short summary of fleet composition (i.e. boat types), gear types, species targeted, and fishing grounds (one paragraph).
---->
-
-### Ecosystem Considerations or climate indicators {#sec-eco-indicators}
-
-<!---
-If this section is not relevant, please state "Ecosystem considerations and/or climate indicators were not included in this assessment."
---->
-
diff --git a/inst/templates/skeleton/modeling_approach.qmd b/inst/templates/skeleton/modeling_approach.qmd
deleted file mode 100644
index cfaaae74..00000000
--- a/inst/templates/skeleton/modeling_approach.qmd
+++ /dev/null
@@ -1,47 +0,0 @@
-## Modeling Approach {#sec-modeling-approach}
-
-### Current Approach {#sec-current-approach}
-
-<!---
-This is a potential automated subsection which will dynamically changed according to the assessment model used to perform the analysis. 
-
-Please provide a short, general overview of platform including reference to the model's paper or online reference.
---->
-
-### Configuration {#sec-configuration}
-
-<!---
-- Time blocks
-- Spatial structure and considerations
-- Growth differnces/morphs
-- Parameters to estimate and parameters to fix
-- Bayesian priors (for which parameters, distributions assumed, and starting values and bounds)
-- Catchability
-- Selectivity
-- Retention
-- Likelihood (penalty, reweighting, ect.)
---->
-
-### Sensitivity Analyses {#sec-model-sensitivity-analyses}
-
-<!---
-Descriptions of which sensitivity analysis to be performed. (i.e. which parameters or data input streams changed in different setups of the model and why)
---->
-
-### Management Benchmarks {#sec-management-benchmarks}
-
-<!---
-Description decisions on management metrics/benchmarks.
---->
-
-### Diagnostics {#sec-diagnostics}
-
-<!---
-Description of which diagnostics will be used.
---->
-
-### Projection Scenarios {#sec-projection-scenarios}
-
-<!---
-Description of which projection scenarios will be run and how the projections will be set up.
---->
diff --git a/inst/templates/skeleton/projections.qmd b/inst/templates/skeleton/projections.qmd
deleted file mode 100644
index c1966c93..00000000
--- a/inst/templates/skeleton/projections.qmd
+++ /dev/null
@@ -1,5 +0,0 @@
-## Projections {#sec-projections}
-
-<!---
-Description of stock status, biological reference points (BRPs), and trends for each scenario; include rebuilding times
---->
diff --git a/inst/templates/skeleton/results.qmd b/inst/templates/skeleton/results.qmd
deleted file mode 100644
index d7a81e3c..00000000
--- a/inst/templates/skeleton/results.qmd
+++ /dev/null
@@ -1,43 +0,0 @@
-## Results {#sec-results}
-
-### Parameter Estimates {#sec-parameter-estimates}
-
-<!---
-Table of the parameters that were estimated and text interpretation as needed; includes Bayesian parameter fit values.
---->
-
-### Recruitment Estimates and Deviations {#recruitment-estimates}
-
-<!---
-Interpretation of the spawner-recruit curve estimation, challenges or issues, and any interpretation of recruitment deviations (i.e. if there is a pattern indicating regime shift, ect.)
---->
-
-### Model Fits {#sec-model-fits}
-
-<!---
-- Indices
-- Composition data
-- Selectivity and retention
-- Catchability
-- Catch
-- Other metrics (if applicable) - discards, environmental data, ect.
---->
-
-### Model Diagnostics {#sec-model-diagnostics}
-
-<!---
-Where applicable:
-- Bridging analysis
-- Correlation analysis
-- Profile likelihoods
-- Jitter analysis
-- Retrospective analysis
---->
-
-### Sensitivity Analysis {#sec-res-sensitivity-analyses}
-
-<!---
-Results and comparison with the base model; each scenario result and what was changed; please include key metrics from each scenario such as steepness (h), R0, Bcurrent, Fcurrent, F/Fmsy, B/Bmsy, ect.
---->
-
-
diff --git a/tests/testthat/test-add_section.R b/tests/testthat/test-add_section.R
index c6675c6b..17489434 100644
--- a/tests/testthat/test-add_section.R
+++ b/tests/testthat/test-add_section.R
@@ -1,35 +1,48 @@
 test_that("Adding new sections works.", {
-  sec_list <- add_base_section(c("introduction", "modeling approach", "results", "discussion"))
+  sec_list <- add_base_section(c("introduction", "assessment", "discussion"))
   sections <- add_section(
-    sec_names = c("abstract", "ecosystem_considerations", "alt_models"),
-    location = c("before-introduction", "after-discussion", "after-model"),
-    other_sections = sec_list,
+    new_section = c("abstract", "ecosystem_considerations", "alt_models"),
+    section_location = c("before-introduction", "after-discussion", "after-assessment"),
+    custom_sections = sec_list,
     subdir = tempdir()
   )
   exp_list <- list(
     "abstract.qmd",
-    "introduction.qmd",
-    "modeling_approach.qmd",
+    "02_introduction.qmd",
+    "04a_assessment-configuration.qmd",
+    "04b_assessment-results.qmd",
+    "04c_assessment-sensitivity.qmd",
+    "04d_assessment-benchmarks.qmd",
+    "04e_assessment-projections.qmd",
     "alt_models.qmd",
-    "results.qmd",
-    "discussion.qmd",
+    "05_discussion.qmd",
     "ecosystem_considerations.qmd"
   )
   expect_equal(sections, exp_list)
 })
 
 test_that("Adding new sections does not work.", {
-  sec_list <- add_base_section(c("introduction", "data", "modeling approach", "acknowledgments", "appendix", "references"))
+  sec_list <- add_base_section(c("introduction", "data", "assessment", "acknowledgments", "appendix", "references"))
   sections <- add_section(
-    sec_names = c("Harvest Control Rules", "Regional Management Considerations", "Research and Data Needs"),
-    location = c("after-model", "after-model", "after-model"),
-    other_sections = sec_list,
+    new_section = c("Harvest Control Rules", "Regional Management Considerations", "Research and Data Needs"),
+    section_location = c("after-assessment", "after-assessment", "after-assessment"),
+    custom_sections = sec_list,
     subdir = tempdir()
   )
   exp_list <- list(
-    "introduction.qmd", "data.qmd", "modeling_approach.qmd", "Harvest_Control_Rules.qmd",
-    "Regional_Management_Considerations.qmd", "Research_and_Data_Needs.qmd",
-    "acknowledgments.qmd", "appendix.qmd", "references.qmd"
+    "02_introduction.qmd",
+    "03_data.qmd",
+    "04a_assessment-configuration.qmd",
+    "04b_assessment-results.qmd",
+    "04c_assessment-sensitivity.qmd",
+    "04d_assessment-benchmarks.qmd",
+    "04e_assessment-projections.qmd",
+    "harvest_control_rules.qmd",
+    "regional_management_considerations.qmd",
+    "research_and_data_needs.qmd",
+    "06_acknowledgments.qmd",
+    "11_appendix.qmd",
+    "07_references.qmd"
   )
   expect_equal(sections, exp_list)
 })
diff --git a/tests/testthat/test-create_template.R b/tests/testthat/test-create_template.R
index dfaa07f0..7f07cc2e 100644
--- a/tests/testthat/test-create_template.R
+++ b/tests/testthat/test-create_template.R
@@ -1,20 +1,22 @@
 test_that("Can trace template files from package", {
   path <- system.file("templates", "skeleton", package = "asar")
   base_temp_files <- c(
-    "acknowledgments.qmd",
-    "appendix.qmd",
-    "assessment_glossaries.tex",
-    "data.qmd",
-    "discussion.qmd",
-    "executive_summary.qmd",
-    # "figures.qmd",
+    "01_executive_summary.qmd",
+    "02_introduction.qmd",
+    "03_data.qmd",
+    "04a_assessment-configuration.qmd",
+    "04b_assessment-results.qmd",
+    "04c_assessment-sensitivity.qmd",
+    "04d_assessment-benchmarks.qmd",
+    "04e_assessment-projections.qmd",
+    "05_discussion.qmd",
+    "06_acknowledgments.qmd",
+    "07_references.qmd",
+    "10_notes.qmd",
+    "11_appendix.qmd"
+    # "09_figures.qmd",
     # "in-header.tex",
-    "introduction.qmd",
-    "modeling_approach.qmd",
-    "projections.qmd",
-    "references.qmd",
-    "results.qmd"
-    # "tables.qmd",
+    # "08_tables.qmd",
     # "title.tex"
   )
   expect_equal(list.files(path), base_temp_files)
@@ -23,22 +25,24 @@ test_that("Can trace template files from package", {
 test_that("create_template() creates correct files", {
   # Define expected report files
   expect_report_files <- c(
-    "acknowledgments.qmd",
-    "appendix.qmd",
-    "assessment_glossaries.tex",
-    "data.qmd",
-    "discussion.qmd",
-    "executive_summary.qmd",
-    "figures.qmd",
-    "introduction.qmd",
-    "modeling_approach.qmd",
-    "projections.qmd",
-    "references.qmd",
-    "results.qmd",
+    "01_executive_summary.qmd",
+    "02_introduction.qmd",
+    "03_data.qmd",
+    "04a_assessment-configuration.qmd",
+    "04b_assessment-results.qmd",
+    "04c_assessment-sensitivity.qmd",
+    "04d_assessment-benchmarks.qmd",
+    "04e_assessment-projections.qmd",
+    "05_discussion.qmd",
+    "06_acknowledgments.qmd",
+    "07_references.qmd",
+    "08_tables.qmd",
+    "09_figures.qmd",
+    "10_notes.qmd",
+    "11_appendix.qmd",
     "SAR_species_skeleton.qmd",
-    "support_files",
-    "tables.qmd"
-  )
+    "support_files"
+    )
 
   # Define expected support files
   expect_support_files <- c(
@@ -57,7 +61,8 @@ test_that("create_template() creates correct files", {
   object_report_files <- list.files(no_inputs_output_path)
   object_support_files <- list.files(file.path(no_inputs_output_path, "support_files"))
 
-  on.exit(unlink(file.path(path, "stock_assessment_reports"), recursive = TRUE), add = TRUE)
+  on.exit(unlink(file.path(path, "stock_assessment_reports"),
+                 recursive = TRUE), add = TRUE)
   # Check if all expected report files are created
   expect_true(all(sort(expect_report_files) == sort(object_report_files)))
 
@@ -79,7 +84,7 @@ test_that("create_template() creates correct files", {
     author = c("John Snow", "Danny Phantom", "Patrick Star"),
     include_affiliation = TRUE,
     parameters = FALSE,
-    resdir = NULL,
+    resdir = "data",
     model_results = "Report.sso",
     model = "SS3"
   )
@@ -91,21 +96,23 @@ test_that("create_template() creates correct files", {
   on.exit(unlink(file.path(path, "stock_assessment_reports"), recursive = TRUE), add = TRUE)
   # Define expected report files for Dover sole
   expect_report_files <- c(
-    "acknowledgments.qmd",
-    "appendix.qmd",
-    "assessment_glossaries.tex",
-    "data.qmd",
-    "discussion.qmd",
-    "executive_summary.qmd",
-    "figures.qmd",
-    "introduction.qmd",
-    "modeling_approach.qmd",
-    "projections.qmd",
-    "references.qmd",
-    "results.qmd",
+    "01_executive_summary.qmd",
+    "02_introduction.qmd",
+    "03_data.qmd",
+    "04a_assessment-configuration.qmd",
+    "04b_assessment-results.qmd",
+    "04c_assessment-sensitivity.qmd",
+    "04d_assessment-benchmarks.qmd",
+    "04e_assessment-projections.qmd",
+    "05_discussion.qmd",
+    "06_acknowledgments.qmd",
+    "07_references.qmd",
+    "08_tables.qmd",
+    "09_figures.qmd",
+    "10_notes.qmd",
+    "11_appendix.qmd",
     "SAR_Dover_sole_skeleton.qmd",
-    "support_files",
-    "tables.qmd"
+    "support_files"
   )
   # Define expected support files for Dover sole
   expect_dover_sole_support_files <- c(
@@ -142,7 +149,8 @@ test_that("warning is triggered for missing models", {
     ),
     regexp = "Results file or model name not defined."
   )
-  on.exit(unlink(file.path(getwd(), "stock_assessment_reports"), recursive = TRUE), add = TRUE)
+  on.exit(unlink(file.path(getwd(), "stock_assessment_reports"),
+                 recursive = TRUE), add = TRUE)
 })
 
 test_that("warning is triggered for existing files", {
@@ -156,7 +164,7 @@ test_that("warning is triggered for existing files", {
     author = c("John Snow", "Danny Phantom", "Patrick Star"),
     include_affiliation = TRUE,
     parameters = FALSE,
-    resdir = NULL,
+    resdir = "data",
     model_results = "Report.sso",
     model = "SS3"
   )
@@ -179,7 +187,7 @@ test_that("warning is triggered for existing files", {
       author = c("John Snow", "Danny Phantom", "Patrick Star"),
       include_affiliation = TRUE,
       parameters = FALSE,
-      resdir = NULL,
+      resdir = "data",
       model_results = "Report.sso",
       model = "SS3"
     ),
@@ -210,7 +218,7 @@ test_that("file_dir works", {
     author = c("John Snow", "Danny Phantom", "Patrick Star"),
     include_affiliation = TRUE,
     parameters = FALSE,
-    resdir = NULL,
+    resdir = "data",
     model_results = "Report.sso",
     model = "SS3",
     file_dir = dir
@@ -218,5 +226,8 @@ test_that("file_dir works", {
 
   file_path <- file.path(dir, "stock_assessment_reports", office, species, year)
   expect_gt(length(list.files(file_path)), 1)
+
+  expect_gte(length(list.files(dir)), 1)
+
   on.exit(unlink(dir, recursive = TRUE), add = TRUE)
 })