diff --git a/.gitignore b/.gitignore
index 0a03c95..db43345 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,3 +34,4 @@ vignettes/*.pdf
 *.knit.md
 .Rproj.user
 
+*.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
index f63ebed..97bd90b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,11 +9,11 @@ Description: Managing, inspecting and sourcing remote repositories such as githu
 Depends:
   R (>= 2.3.0)
 Imports: 
-  jsonlite,jsTree,miniUI,shiny,httr,utils,tools,plyr,crayon
+  httr,utils,crayon,tools,rstudioapi
 License: GPL-2 | GPL-3
 URL: https://github.com/metrumresearchgroup/vcs
 BugReports: https://github.com/metrumresearchgroup/options/issues
 LazyData: true
 NeedsCompilation: no
 Packaged: 2017-06-08 14:00:00 UTC; Yoni
-RoxygenNote: 6.0.1.9000
+RoxygenNote: 6.0.1
diff --git a/NAMESPACE b/NAMESPACE
index 757b945..b618922 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,8 +8,6 @@ export(grepr)
 export(gsubr)
 export(list_repos)
 export(ls_remote)
-export(navigate_remote)
-export(sasha)
 export(setwd_remote)
 export(source_remote)
 export(sparse_checkout)
@@ -21,33 +19,6 @@ importFrom(httr,add_headers)
 importFrom(httr,content)
 importFrom(httr,http_error)
 importFrom(httr,parse_url)
-importFrom(jsTree,jsTree)
-importFrom(jsTree,jsTreeOutput)
-importFrom(jsTree,renderJsTree)
-importFrom(jsonlite,fromJSON)
-importFrom(miniUI,gadgetTitleBar)
-importFrom(miniUI,miniContentPanel)
-importFrom(miniUI,miniPage)
-importFrom(miniUI,miniTitleBarButton)
-importFrom(shiny,actionButton)
-importFrom(shiny,conditionalPanel)
-importFrom(shiny,eventReactive)
-importFrom(shiny,isolate)
-importFrom(shiny,observeEvent)
-importFrom(shiny,paneViewer)
-importFrom(shiny,radioButtons)
-importFrom(shiny,reactiveValues)
-importFrom(shiny,renderPrint)
-importFrom(shiny,renderUI)
-importFrom(shiny,runGadget)
-importFrom(shiny,selectInput)
-importFrom(shiny,sidebarLayout)
-importFrom(shiny,sidebarPanel)
-importFrom(shiny,stopApp)
-importFrom(shiny,textInput)
-importFrom(shiny,uiOutput)
-importFrom(shiny,verbatimTextOutput)
-importFrom(shiny,wellPanel)
 importFrom(tools,file_path_as_absolute)
 importFrom(utils,head)
 importFrom(utils,tail)
diff --git a/R/grep_remote.R b/R/grep_remote.R
index 8e2e861..bf8565a 100644
--- a/R/grep_remote.R
+++ b/R/grep_remote.R
@@ -3,10 +3,12 @@
 #' @param pattern   character, string containing a regular expression
 #' @param path      character, path to search, see details
 #' @param recursive boolean, Should the listing recurse into directories? passed to list.files, Default: FALSE
-#' @param whole_word boolean, if TRUE then the pattern will be wrapped with \\bpattern\\b internally, Default: FALSE
+#' @param ...       arguments passed to grep
+#' @param whole_word boolean, if TRUE then the pattern will be 
+#'   wrapped with \\bpattern\\b internally, Default: FALSE
 #' @param padding   integer, number of rows to return in addition to the query line, Default: 5
 #' @param use_crayon boolean, use crayon colors in console output, Default: TRUE
-#' @param ...       arguments passed to grep
+#' @param marker boolean, use rstudioapi marker, Default: interactive()
 #' @return grepr(value = FALSE) returns a vector of the indices of the elements of x 
 #' that yielded a match (or not, for invert = TRUE. 
 #' This will be an integer vector unless the input is a long vector, when it will be a double vector.
@@ -26,14 +28,21 @@
 #' grepr(pattern = 'importFrom',path = remotepath,value=TRUE)
 #' grepr(pattern = 'importFrom',path = remotepath,value=TRUE,padding=3)
 #' grepr(pattern = 'tags$script',
-#'       path = list(path = 'timelyportfolio/vueR',subdir='R|inst',vcs='github'),
+#'       path = list(path = 'timelyportfolio/vueR',subdir='R|inst',vcs='github',PAT = Sys.getenv('GITHUB_PAT')),
 #' padding=3,value=TRUE,fixed=TRUE)}
 #' @export
 #' @importFrom httr content GET parse_url
 #' @importFrom utils tail head
 #' @importFrom crayon green red
-#' @importFrom jsTree jsTree
-grepr <- function(pattern,path,recursive=FALSE, whole_word = FALSE, padding=0,use_crayon = TRUE, interactive=FALSE,marker = FALSE, ...){
+grepr <- function(pattern,
+                  path,
+                  recursive=FALSE,
+                  ... ,
+                  whole_word = FALSE,
+                  padding=1,
+                  use_crayon = TRUE,
+                  marker = interactive()
+                  ){
 
   if(marker)
     use_crayon <- FALSE
@@ -69,7 +78,9 @@ grepr <- function(pattern,path,recursive=FALSE, whole_word = FALSE, padding=0,us
   out=sapply(fl,function(x){
     args=grepVars
     args$pattern=pattern
-    if(is.null(args$value)||interactive) args$value=FALSE
+    if(is.null(args$value)){
+      args$value <- FALSE 
+    }
     
     args$x=switch(vcs,
             local= {readLines(x,warn = FALSE)},
@@ -79,7 +90,7 @@ grepr <- function(pattern,path,recursive=FALSE, whole_word = FALSE, padding=0,us
               s <- httr::content(
                       httr::GET(x,
                         httr::add_headers(
-                          Authorization = sprintf('token %s',Sys.getenv('GHE_PAT'))
+                          Authorization = sprintf('token %s',path$PAT)
                         )
                       )
                     )
@@ -122,7 +133,7 @@ grepr <- function(pattern,path,recursive=FALSE, whole_word = FALSE, padding=0,us
         } 
         gdx=sapply(g,function(x,pad,nmax) seq(from=pmax(1,x-pad),to=pmin(nmax,x+pad)),pad=padding,nmax=length(args$x))
         out=unique(unlist(sapply(gdx,function(i){
-          if(use_crayon&!interactive){
+          if(use_crayon){
             ifelse(i%in%g0,{
               
               this_pat <- regexpr(pattern, args$x[i])
@@ -146,22 +157,6 @@ grepr <- function(pattern,path,recursive=FALSE, whole_word = FALSE, padding=0,us
     } 
   })
   
-  if(interactive & vcs%in%c('ghe','github','bitbucket') ){
-    
-    s0 <- out[sapply(out,length)>0]
-
-    NAMES <- gsub(sprintf('^(.*?)%s/|\\?(.*?)$',path$branch),'',names(s0))
-    
-    tree <- jsTree::jsTree$new(ls_remote(path$path,vcs=vcs))
-    
-    tree$current_nodestate <- tree$data%in%NAMES
-    tree$add_vcs(remote_repo = path$path,vcs = vcs,remote_branch = 'master')
-    tree$raw_token <- ghe_raw_token(path = path$path,file = tree$data[1],myPAT = Sys.getenv('GHE_PAT'))
-    tree$preview_search <- pattern
-    
-    tree$show()
-    
-  }else{
     out <- out[sapply(out,length)>0]
     
     if(!marker){
@@ -173,7 +168,7 @@ grepr <- function(pattern,path,recursive=FALSE, whole_word = FALSE, padding=0,us
     }
     
     invisible(out)
-  }
+  
   
 }
 
diff --git a/R/ls_remote.R b/R/ls_remote.R
index d0bec21..8be1bc6 100644
--- a/R/ls_remote.R
+++ b/R/ls_remote.R
@@ -21,18 +21,25 @@
 #'    #'master' branch
 #'     ls_remote('metrumrg/qapply',vcs='bitbucket')
 #' 
-ls_remote <- function(path=getwd(),branch='master',subdir=NULL,vcs='github', full.names=FALSE){
+ls_remote <- function(
+  path=getwd(),
+  branch='master',
+  subdir=NULL,
+  vcs='github', 
+  full.names=FALSE, 
+  PAT = Sys.getenv('GITHUB_PAT')
+  ){
+  
   this_wd <- getwd()
+  
   switch(vcs,
          ghe={
-           
-           myPAT <- Sys.getenv('GHE_PAT')
-           
+
            get_git <- sprintf('https://ghe.metrumrg.com/api/v3/repos/%s/git/trees/%s?recursive=1',path,branch)
            
            x <- httr::GET(get_git,
                           httr::add_headers(
-                            Authorization = sprintf('token %s',myPAT)
+                            Authorization = sprintf('token %s',PAT)
                           )
            )
            
@@ -62,15 +69,13 @@ ls_remote <- function(path=getwd(),branch='master',subdir=NULL,vcs='github', ful
            
          },
          github={
-           
-           myPAT <- Sys.getenv('GITHUB_PAT')
-           
+
            uri_git <- sprintf('https://api.github.com/repos/%s',path)
            get_git <- sprintf('https://api.github.com/repos/%s/git/trees/%s%s',path,branch,'?recursive=1')
            
-           if(nzchar(myPAT)){
-             uri_git <- sprintf('%s?access_token=%s',uri_git,Sys.getenv('GITHUB_PAT'))
-             get_git <- sprintf('%s&access_token=%s',get_git,Sys.getenv('GITHUB_PAT'))
+           if(nzchar(PAT)){
+             uri_git <- sprintf('%s?access_token=%s',uri_git,PAT)
+             get_git <- sprintf('%s&access_token=%s',get_git,PAT)
              }
            
            chk_git <- httr::http_error(uri_git)
@@ -92,8 +97,8 @@ ls_remote <- function(path=getwd(),branch='master',subdir=NULL,vcs='github', ful
              
               raw_git <- sprintf('https://raw.githubusercontent.com/%s/%s/%s',path,branch,s) 
              
-              if(nzchar(myPAT)){
-               dlPAT <- gsub('^(.*?)\\?','',httr::content(httr::GET(sprintf('https://api.github.com/repos/%s/contents/%s?access_token=%s',path,s[1],myPAT)))$download_url)
+              if(nzchar(PAT)){
+               dlPAT <- gsub('^(.*?)\\?','',httr::content(httr::GET(sprintf('https://api.github.com/repos/%s/contents/%s?access_token=%s',path,s[1],PAT)))$download_url)
                if(!dlPAT%in%raw_git)
                 raw_git <- sprintf('%s?%s',raw_git,dlPAT)
               }
diff --git a/R/make_marker.R b/R/make_marker.R
index 5426d01..0020cea 100644
--- a/R/make_marker.R
+++ b/R/make_marker.R
@@ -16,8 +16,9 @@ make_marker <- function(pattern,x){
                         
                       lapply(x[[nx]],function(xx){
                         r <- as.numeric(gsub('\\D','',gsub(':(.*?)$','',xx)))
+                        type <- ifelse(grepl('\\[',gsub(':(.*?)$','',xx)),'info','usage')
                         l <- gsub('^(.*?):','',xx)
-                        list(type='info',file=new_nx,line=r,column=1,message=l) 
+                        list(type=type,file=new_nx,line=r,column=1,message=l) 
                       })
                     }),recursive = FALSE),
                     basePath = getwd(),
diff --git a/R/navigate_remote.R b/R/navigate_remote.R
deleted file mode 100644
index 01fd88e..0000000
--- a/R/navigate_remote.R
+++ /dev/null
@@ -1,30 +0,0 @@
-#' @title Visually inspect structure of git repository before initial fetch
-#' @description Visually inpsect the directory structure of it before cloning/fetching/pulling
-#' @param path character, Path to root directory of git repository or a name of a github/bitbucket repository, Default: setwd()
-#' @param branch character, alias of the github/bitbucket branch to retrieve directory structure, Default: 'master'
-#' @param vcs character, choose which version control system to search (github, bitbucket, git (head of checkout repo), svn), Default: 'github'
-#' @param show_tree boolean, show jsTree widget output in viewer, Default: TRUE
-#' @details 
-#' By default path assumes a local address, if path is a valid repository name eg 'tidyverse/glue' 
-#' then the pattern is checked on the specified pulic github repository
-#' @return widget
-#' @export
-#' @importFrom jsTree jsTree
-#' @examples 
-#' navigate_remote('tidyverse/glue')
-#' navigate_remote('tidyverse/glue',branch='named_args')
-#' @seealso
-#'  \code{\link[jsTree]{jsTree}}
-navigate_remote <- function(path=getwd(), branch='master', vcs='github', show_tree = TRUE){
-
-  tree <- jsTree::jsTree$new(ls_remote(path = path,branch = branch,vcs = vcs))
-
-  tree$add_vcs(remote_repo = path,vcs = vcs,remote_branch = branch)
-
-  if(show_tree){
-    tree$show()
-  }else{
-    invisible(tree)
-  }
-    
-}
\ No newline at end of file
diff --git a/R/sasha.R b/R/sasha.R
deleted file mode 100644
index 83a1b14..0000000
--- a/R/sasha.R
+++ /dev/null
@@ -1,218 +0,0 @@
-#' @title vcs UI
-#' @description Shiny gadget for controlling, navigating and maintaining version control directories on local and remote repositories
-#' @param rootpath root path to look for version control directories, Default: getwd()
-#' @return nothing
-#' @details Version control systems that can be accessed are git, github, bitbucket and svn. Throught this gadget you can do full and sparse checkout and update current vcs directory. 
-#' @examples 
-#' \dontrun{
-#' if(interactive()){
-#'  sasha(getwd())
-#'  }
-#' }
-#' @seealso 
-#'  \code{\link[jsonlite]{fromJSON}}
-
-#'  \code{\link[jsTree]{jsTreeOutput}},\code{\link[jsTree]{renderJsTree}}
-
-#'  \code{\link[miniUI]{miniPage}},\code{\link[miniUI]{gadgetTitleBar}},\code{\link[miniUI]{miniTitleBarButton}},\code{\link[miniUI]{miniContentPanel}}
-
-#'  \code{\link[shiny]{sidebarLayout}},\code{\link[shiny]{sidebarPanel}},\code{\link[shiny]{radioButtons}},\code{\link[shiny]{conditionalPanel}},\code{\link[shiny]{wellPanel}},\code{\link[shiny]{textInput}},\code{\link[shiny]{uiOutput}},\code{\link[shiny]{actionButton}},\code{\link[shiny]{reactiveValues}},\code{\link[shiny]{observeEvent}},\code{\link[shiny]{renderPrint}},\code{\link[shiny]{eventReactive}},\code{\link[shiny]{isolate}},\code{\link[shiny]{renderUI}},\code{\link[shiny]{verbatimTextOutput}},\code{\link[shiny]{selectInput}},\code{\link[shiny]{stopApp}},\code{\link[shiny]{runGadget}},\code{\link[shiny]{paneViewer}}
-
-#'  \code{\link[vcs]{find.remote}},\code{\link[vcs]{diff_head}},\code{\link[vcs]{navigate_remote}},\code{\link[vcs]{sparse_checkout}}
-#' @rdname sasha
-#' @export 
-#' @importFrom jsonlite fromJSON
-#' @importFrom jsTree jsTreeOutput renderJsTree
-#' @importFrom miniUI miniPage gadgetTitleBar miniTitleBarButton miniContentPanel
-#' @importFrom shiny sidebarLayout sidebarPanel radioButtons conditionalPanel wellPanel textInput uiOutput actionButton reactiveValues observeEvent renderPrint eventReactive isolate renderUI verbatimTextOutput selectInput stopApp runGadget paneViewer
-sasha<-function(rootpath=getwd()){
-ui <- miniUI::miniPage(
-  miniUI::gadgetTitleBar('SASHA',
-                         left = miniUI::miniTitleBarButton(inputId = "qt","Quit",primary = TRUE),
-                         right=NULL),
-  miniUI::miniContentPanel(
-    shiny::sidebarLayout(sidebarPanel = 
-                           shiny::sidebarPanel(
-                             shiny::radioButtons(inputId = 'dirType',label = 'Source',choices = c('Local','Remote'),selected = 'Local',inline = TRUE),
-                             shiny::conditionalPanel("input.dirType=='Local'",{
-                               shiny::wellPanel(
-                                 shiny::textInput(inputId = 'localPath',label = 'Root Directory',placeholder = 'Enter Root Directory',value = rootpath),
-                                 shiny::uiOutput('localDir'),
-                                 shiny::actionButton('updateRepo','Update Checkout'))  
-      }),
-      shiny::conditionalPanel("input.dirType=='Remote'",{
-        shiny::wellPanel(
-          shiny::textInput(inputId='remotePath',label = 'Remote Repository'),
-          shiny::radioButtons(inputId = 'vcs',label = 'Remote Version Control Sytem',choices = c('git','github','bitbucket','svn'),selected = 'github',inline = TRUE),
-          shiny::actionButton('queryRepo','Query Remote Repo'),
-          shiny::textInput('dirOutput','',placeholder = 'Path of Checkout'),
-          shiny::actionButton('createRepo','Create Sparse Checkout'))
-      }),
-      shiny::uiOutput('chosen')
-    ),
-    mainPanel = shiny::mainPanel(
-      shiny::uiOutput('main')
-    ))
-  
-
-))
-
-server <- function(input, output,session) {
-  
-  network <- shiny::reactiveValues()
-  
-  shiny::observeEvent(input$tree_update,{
-    current_selection<-input$tree_update$.current_tree
-    if(!is.null(current_selection)) network$tree <- jsonlite::fromJSON(current_selection)
-  })
-  
-  shiny::observeEvent(network$tree,{
-    output$results <- shiny::renderPrint({
-      str.out=''
-      if(length(network$tree)>0) str.out=network$tree
-      return(str.out)
-    })    
-  })
-  
-  shiny::observeEvent(c(input$f1,input$queryRepo),{
-    output$results <- shiny::renderPrint({
-      str.out=''
-      return(str.out)
-    })    
-  })
-  
-  remote.current<-shiny::eventReactive(input$localPath,{
-    root<-shiny::isolate(input$localPath)
-    find.remote(root) 
-  })
-  
-  shiny::observeEvent(c(remote.current(),input$dirType,input$queryRepo),{
-    
-    output$tree <- switch(input$dirType,
-                          Local={
-                            jsTree::renderJsTree({
-                              vcs_type='git'
-                              rc<-remote.current()
-                              vcs_type=rc[rc$dir==input$f1,'vcs']
-                              opts=NULL
-                              if(!is.null(input$f1)){
-                                
-                                tree <- navigate_remote(isolate(input$f1),vcs=vcs_type, show = FALSE)
-                                
-                              if(dir.exists(input$f1)){
-                                
-                                tree$current_nodestate <- diff_head(isolate(input$f1))
-                                
-                              }
-                              
-                                tree$show()
-                                
-                              }
-                            })
-                          },
-                          Remote={
-                            jsTree::renderJsTree({
-                              if(nchar(isolate(input$remotePath))>0){
-                                shiny::isolate(navigate_remote(input$remotePath,vcs=input$vcs))
-                              }
-                            })
-                          })
-    
-  })
-  
-  shiny::observeEvent(input$f1,{
-    output$main<-shiny::renderUI({
-      if(dir.exists(input$f1)){
-        jsTree::jsTreeOutput(outputId = 'tree',width = '100%',height = 800)
-      }else{
-        p('Directory Not Found') 
-      }
-    })   
-  })
- 
-  shiny::observeEvent(c(input$createRepo),{
-    if(!is.null(input$f1)){
-      switch(input$vcs,
-           github={
-             repo_url<-sprintf('https://github.com/%s.git',input$remotePath)
-             f2<-gsub(sprintf('%s/%s',input$f1,'master'),'',network$tree)
-             queries<-gsub('^(.*?)master/','',f2)
-             this.vcs<-'git'
-           },
-           bitbucket={
-             repo_url<-sprintf('https://bitbucket.com/%s.git',input$remotePath)
-             f2<-gsub(sprintf('%s/%s',input$f1,'master'),'',network$tree)
-             queries<-gsub('^(.*?)master/','',f2)
-             this.vcs<-'git'
-           },
-           svn={
-             repo_url<-sprintf('svn+ssh://%s',input$remotePath)
-             f2<-gsub(sprintf('%s/%s',input$f1,'master'),'',network$tree)
-             this.vcs<-'svn'
-           })
-        
-        # if(dir.exists(sprintf('%s/.git',input$dirOutput))){
-        #   sparse_checkout(repo_url = repo_url,
-        #                        vcs = this.vcs,
-        #                        queries = queries,
-        #                        dest.dir = input$dirOutput,
-        #                        create = FALSE,
-        #                        append = FALSE)
-        # }else{
-          sparse_checkout(repo_url = repo_url,
-                               vcs = this.vcs,
-                               queries = queries,
-                               dest.dir = input$dirOutput,
-                               create = TRUE)
-        #}
-       
-    }
-  })
-  
-  shiny::observeEvent(c(input$updateRepo),{
-    
-    rc<-remote.current()
-    this.vcs=rc[rc$dir==input$f1,'vcs']
-    if(!is.null(input$f1)){
-      switch(this.vcs,
-             git={
-               repo_url<-sprintf('https://github.com/%s.git',input$remotePath)
-               f2<-gsub(sprintf('%s/%s',input$f1,'master'),'',network$tree)
-               queries<-gsub('^(.*?)master/','',f2)
-               this.vcs<-'git'
-             },
-             svn={
-               repo_url<-sprintf('svn+ssh://%s',input$remotePath)
-               f2<-gsub(sprintf('%s/%s',input$f1,'master'),'',network$tree)
-               this.vcs<-'svn'
-             })
-      if(dir.exists(sprintf('%s/.%s',input$f1,this.vcs))){
-        sparse_checkout(repo_url = repo_url,
-                             vcs = this.vcs,
-                             queries = queries,
-                             dest.dir = input$f1,
-                             create = FALSE,
-                             append = FALSE)
-      }
-      
-    }
-  })
-  
-  
-  output$chosen=shiny::renderUI({
-    shiny::verbatimTextOutput(outputId = "results")
-  })
-  
-  output$localDir<-shiny::renderUI({
-    rc<-remote.current()
-    shiny::selectInput(inputId = 'f1',
-                       label = 'Choose Local Repository',
-                       choices = rc$dir,
-                       selected = rc$dir[1])
-  })
-  
-  shiny::observeEvent(input$qt,{shiny::stopApp()})
-}
-
-shiny::runGadget(ui, server, viewer = shiny::paneViewer(minHeight = 450))
-}
\ No newline at end of file
diff --git a/R/utils.R b/R/utils.R
index 4705500..020ac32 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,11 +1,11 @@
 #' @export
-ghe_raw_token <- function(path,file,myPAT = Sys.getenv('GHE_PAT')){
+ghe_raw_token <- function(path,file,PAT = Sys.getenv('GHE_PAT')){
   
   dl_git <- sprintf('https://ghe.metrumrg.com/api/v3/repos/%s/contents/%s',path,file)
   
   x1 <- httr::GET(dl_git,
                   httr::add_headers(
-                    Authorization = sprintf('token %s',myPAT)
+                    Authorization = sprintf('token %s',PAT)
                   )
   )
   
diff --git a/README.md b/README.md
index a56e8bd..9eba056 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,6 @@ devtools::install_github('metrumresearchgroup/vcs')
   - **gsubr**: run recursive gsub directly on local paths
   - **list_repos**: list repositories of a user in a version control repository
   - **ls_remote**: list files on remote branches on a version control repository
-  - **navigate_remote**: visualize the structure of a remote branch prior to cloning/forking
   - **setwd_remote**: replace inline script from local path to remote path
   - **source_remote**: source script on remote branches, works for reading in data on remote and nested sourcing
 
@@ -22,44 +21,3 @@ devtools::install_github('metrumresearchgroup/vcs')
   - **diff_head**: query the difference in files between current fetch and the HEAD of a repository
   - **sparse_checkout**: create a sparse checkout of a repository on github/bitbucket/svn
   - **update_depth**: if the git repository was checked out with a depth setting, use this function to update or cancel the depth setting
-
-## GUI
-
-### Interactive recursive grep
-
-  - Run recursive grep directly on remote branches of Github/Bitbucket/SVN and inspect the results using an interactive UI.
-  - Preview* text files in the branch without needing to checkout (Github/BitBucket only)
-  - The search term inputed will be used in the preview in a search textbox to highlight the term in document. The user can then continue and use the search box to search for other terms int he text. 
-
-![](https://github.com/yonicd/jsTree/blob/master/Miscellaneous/jstree_vcs_grepr.gif?raw=true)
-
-### Sasha
-
-Alexa for R!
-
-Let Sasha help you control your version control repositories both on your checkouts and on the master. Just point Sasha to a root path where the repositories are set and the rest is done for you. 
-
-  - Toggle between local checkouts and remote repos
-  
-  - Local
-  
-    - Auto recognition of svn and git parent folders
-    - Checks to see what the current (sparse) checkout is compared to HEAD
-    - Users can update the definitions of the (sparse) checkout through the GUI
-    
-  - Remote
-    - Navigate to any online repository on Github, Bitbucket or SVN
-    - View the structure of a branch in the repo
-    - Preview* text files in the branch without needing to checkout (Github/BitBucket only)
-    - Search within previewed file for text
-    - Select files to create (sparse) checkout and check them out to local path of choice
-
-![](https://github.com/yonicd/vcs/blob/master/Miscellaneous/sasha.gif?raw=true)
-
-### *Limitations
-
-  Limitations of the the internal viewer of RStudio Preview and how it limits the functionality of the [jsTree](https://github.com/metrumresearchgroup/jsTree) package (that is the engine of the VCS GUI): 
-
-  - **mac OS** internal viewer does not allow for user defined context menus. So you can't right click on a file in the tree and preview, you need to use the preview button above the tree. This forces you to preview the first file it finds with a filled checkbox.
-  - **windows OS** internal viewer does not allow to read files from online so no preview.
-  
\ No newline at end of file
diff --git a/man/grepr.Rd b/man/grepr.Rd
index 8a84345..dbc2dfa 100644
--- a/man/grepr.Rd
+++ b/man/grepr.Rd
@@ -4,8 +4,8 @@
 \alias{grepr}
 \title{Recursive grep}
 \usage{
-grepr(pattern, path, recursive = FALSE, whole_word = FALSE, padding = 0,
-  use_crayon = TRUE, interactive = FALSE, marker = FALSE, ...)
+grepr(pattern, path, recursive = FALSE, ..., whole_word = FALSE,
+  padding = 1, use_crayon = TRUE, marker = interactive())
 }
 \arguments{
 \item{pattern}{character, string containing a regular expression}
@@ -14,13 +14,16 @@ grepr(pattern, path, recursive = FALSE, whole_word = FALSE, padding = 0,
 
 \item{recursive}{boolean, Should the listing recurse into directories? passed to list.files, Default: FALSE}
 
-\item{whole_word}{boolean, if TRUE then the pattern will be wrapped with \\bpattern\\b internally, Default: FALSE}
+\item{...}{arguments passed to grep}
+
+\item{whole_word}{boolean, if TRUE then the pattern will be 
+wrapped with \\bpattern\\b internally, Default: FALSE}
 
 \item{padding}{integer, number of rows to return in addition to the query line, Default: 5}
 
 \item{use_crayon}{boolean, use crayon colors in console output, Default: TRUE}
 
-\item{...}{arguments passed to grep}
+\item{marker}{boolean, use rstudioapi marker, Default: interactive()}
 }
 \value{
 grepr(value = FALSE) returns a vector of the indices of the elements of x 
@@ -47,6 +50,6 @@ grepr(pattern = 'importFrom',path = remotepath)
 grepr(pattern = 'importFrom',path = remotepath,value=TRUE)
 grepr(pattern = 'importFrom',path = remotepath,value=TRUE,padding=3)
 grepr(pattern = 'tags$script',
-      path = list(path = 'timelyportfolio/vueR',subdir='R|inst',vcs='github'),
+      path = list(path = 'timelyportfolio/vueR',subdir='R|inst',vcs='github',PAT = Sys.getenv('GITHUB_PAT')),
 padding=3,value=TRUE,fixed=TRUE)}
 }
diff --git a/man/ls_remote.Rd b/man/ls_remote.Rd
index b087c8c..b15f40a 100644
--- a/man/ls_remote.Rd
+++ b/man/ls_remote.Rd
@@ -5,7 +5,7 @@
 \title{Inspect directory structure of version control system repository}
 \usage{
 ls_remote(path = getwd(), branch = "master", subdir = NULL,
-  vcs = "github", full.names = FALSE)
+  vcs = "github", full.names = FALSE, PAT = Sys.getenv("GITHUB_PAT"))
 }
 \arguments{
 \item{path}{character, Path to root directory of git/svn repository or a name of a github/bitbucket repository, Default: setwd()}
diff --git a/man/navigate_remote.Rd b/man/navigate_remote.Rd
deleted file mode 100644
index 1e8dca1..0000000
--- a/man/navigate_remote.Rd
+++ /dev/null
@@ -1,35 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/navigate_remote.R
-\name{navigate_remote}
-\alias{navigate_remote}
-\title{Visually inspect structure of git repository before initial fetch}
-\usage{
-navigate_remote(path = getwd(), branch = "master", vcs = "github",
-  show_tree = TRUE)
-}
-\arguments{
-\item{path}{character, Path to root directory of git repository or a name of a github/bitbucket repository, Default: setwd()}
-
-\item{branch}{character, alias of the github/bitbucket branch to retrieve directory structure, Default: 'master'}
-
-\item{vcs}{character, choose which version control system to search (github, bitbucket, git (head of checkout repo), svn), Default: 'github'}
-
-\item{show_tree}{boolean, show jsTree widget output in viewer, Default: TRUE}
-}
-\value{
-widget
-}
-\description{
-Visually inpsect the directory structure of it before cloning/fetching/pulling
-}
-\details{
-By default path assumes a local address, if path is a valid repository name eg 'tidyverse/glue' 
-then the pattern is checked on the specified pulic github repository
-}
-\examples{
-navigate_remote('tidyverse/glue')
-navigate_remote('tidyverse/glue',branch='named_args')
-}
-\seealso{
-\code{\link[jsTree]{jsTree}}
-}
diff --git a/man/sasha.Rd b/man/sasha.Rd
deleted file mode 100644
index b120d58..0000000
--- a/man/sasha.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/sasha.R
-\name{sasha}
-\alias{sasha}
-\title{vcs UI}
-\usage{
-sasha(rootpath = getwd())
-}
-\arguments{
-\item{rootpath}{root path to look for version control directories, Default: getwd()}
-}
-\value{
-nothing
-}
-\description{
-Shiny gadget for controlling, navigating and maintaining version control directories on local and remote repositories
-}
-\details{
-Version control systems that can be accessed are git, github, bitbucket and svn. Throught this gadget you can do full and sparse checkout and update current vcs directory.
-}
-\examples{
-\dontrun{
-if(interactive()){
- sasha(getwd())
- }
-}
-}
-\seealso{
-\code{\link[jsonlite]{fromJSON}}
- \code{\link[jsTree]{jsTreeOutput}},\code{\link[jsTree]{renderJsTree}}
- \code{\link[miniUI]{miniPage}},\code{\link[miniUI]{gadgetTitleBar}},\code{\link[miniUI]{miniTitleBarButton}},\code{\link[miniUI]{miniContentPanel}}
- \code{\link[shiny]{sidebarLayout}},\code{\link[shiny]{sidebarPanel}},\code{\link[shiny]{radioButtons}},\code{\link[shiny]{conditionalPanel}},\code{\link[shiny]{wellPanel}},\code{\link[shiny]{textInput}},\code{\link[shiny]{uiOutput}},\code{\link[shiny]{actionButton}},\code{\link[shiny]{reactiveValues}},\code{\link[shiny]{observeEvent}},\code{\link[shiny]{renderPrint}},\code{\link[shiny]{eventReactive}},\code{\link[shiny]{isolate}},\code{\link[shiny]{renderUI}},\code{\link[shiny]{verbatimTextOutput}},\code{\link[shiny]{selectInput}},\code{\link[shiny]{stopApp}},\code{\link[shiny]{runGadget}},\code{\link[shiny]{paneViewer}}
- \code{\link[vcs]{find.remote}},\code{\link[vcs]{diff_head}},\code{\link[vcs]{navigate_remote}},\code{\link[vcs]{sparse_checkout}}
-}