Have you read the documentation for readLines or read_lines? They can be found by typing ?readLines or ?read_lines into the r console.
In it they state:
Value:
A character vector of length the number of lines read.
So just using data.frame(readLines(...)) is just going to give you a data frame with a single character column.
I recommend you take a step back from trying to build your shiny ui and figure out how to parse your data in your local R session. If you don't have a firm grasp of what the data will look like, at least generally, then building a ui will be very difficult. I also suggest that you take the time to thoroughly read the documentation for the functions you are using as they typically have a lot of useful information and examples.
As for editing tables, I have never used rhandsontable before, but you can create ui elements that allow them to do things like select columns and filter rows from things like selectInput() and then just do the data frame manipulation in your server code. Again, I recommend you take a step back from the shiny side and figure out how to do this locally outside of the app. Debugging in your local session is much easier comparatively than debugging a shiny app.