adjust config docs to new directory structure (#159)

vignettes/config_yml.Rmd

@@ -82,15 +82,15 @@ The `file_names`{.yaml} section contains options to define the file names of loc
 
 #### filename_abcd
 
-`filename_abcd`{.yaml} is the filename of the file that contains asset based company data, including production values and physical emission intensity values. It must be a single string/character value, and it must refer to a valid, accessible, local file. As an example:
+`filename_abcd`{.yaml} is the filename of the file in the directory defined by `dir_input`{.yaml} that contains asset based company data, including production values and physical emission intensity values. It must be a single string/character value, and it must refer to a valid, accessible, local file. As an example:
 
 ```yaml
     filename_abcd: "2023-02-17_AI_RMI_PACTA for Banks Free dataset_EO_2022Q4.xlsx"
 ```
 
 #### sheet_abcd
 
-`sheet_abcd`{.yaml} is the name of the sheet that contains asset based company data in the file defined by `filename_abcd`{.yaml} and stored in the directory defined by `dir_abcd`{.yaml}. It must be a single string/character value, and it must refer to a valid, accessible, sheet name in the appropriate file. As an example:
+`sheet_abcd`{.yaml} is the name of the sheet that contains asset based company data in the file defined by `filename_abcd`{.yaml} and stored in the directory defined by `dir_input`{.yaml}. It must be a single string/character value, and it must refer to a valid, accessible, sheet name in the appropriate file. As an example:
 
 ```yaml
     sheet_abcd: "Company Indicators - PACTA Comp"
@@ -205,7 +205,7 @@ A full example `sector_split`{.yaml} section might look like:
 
 #### sheet_advanced_company_indicators
 
-`sheet_advanced_company_indicators`{.yaml} is the name of the sheet that contains asset based company production data in the file defined by `filename_advanced_company_indicators`{.yaml} and stored in the directory defined by `dir_advanced_company_indicators`{.yaml}. It must be a single string/character value, and it must refer to a valid, accessible, sheet name in the appropriate file. As an example:
+`sheet_advanced_company_indicators`{.yaml} is the name of the sheet that contains asset based company production data in the file defined by `filename_advanced_company_indicators`{.yaml} and stored in the directory defined by `dir_input`{.yaml}. It must be a single string/character value, and it must refer to a valid, accessible, sheet name in the appropriate file. As an example:
 
 ```yaml
     sheet_advanced_company_indicators: "Company Activities"
@@ -225,7 +225,6 @@ A full example `matching`{.yaml} section might look like:
       join_id: NULL
     manual_sector_classification:
       use_manual_sector_classification: FALSE
-      dir_manual_sector_classification: "path/to/manual_sector_classification_folder"
       filename_manual_sector_classification: "manual_sector_classification.csv"
 ```