make `.nushell/` a proper module (dragoon/komodo!123)

this MR turns `./.nushell/` into a directory module by
- adding `mod.nu`
- exporting all the modules

all uses of `.nushell/` have been fixed to not mention `.nu` internal modules anymore.

> 💡 **Note**  
> the `.nushell venv` module has been removed because, when the `$venv.VENV` activation script is not there, Nushell can't parse the whole `.nushell` module, which is very annoying to have to rely of the state of the external filesystem to be able to simply parse a module...

.nushell/mod.nu

+export module binary.nu
+export module cargo.nu
+export module color.nu
+export module error.nu
+export module formats.nu
+export module fs.nu
+export module math.nu
+export module parse.nu
+export module plot.nu

.nushell/plot.nu

-use venv.nu VENV
-
 export const COMMON_OPTIONS = [
     --x-scale log
     --x-scale-base 2
@@ -70,6 +68,5 @@ export def into-axis-options [-x: string, -y: string]: table<x: float, y: float>
 }
 
 export def --wrapped gplt [...args: string] {
-    overlay use $VENV
     ^gplt ...$args
 }

.nushell/venv.nu

-export const VENV = ($nu.home-path | path join ".local/share/venvs/gplt/bin/activate.nu")

README.md

@@ -25,7 +25,7 @@ Komodo provides a bunch of other binaries that might be interesting of useful to
 
 The easiest is to use the `cargo.nu` Nushell module as follows
 ```bash
-use .nushell/cargo.nu "cargo bin"
+use .nushell cargo "cargo bin"
 help cargo bin
 ```
 

benchmarks/.nushell/commit/plot.nu

-use ../../../.nushell/math.nu *
-use ../../../.nushell/fs.nu check-file
-use ../../../.nushell/plot.nu [ into-axis-options, COMMON_OPTIONS, gplt ]
+use ../../../.nushell math *
+use ../../../.nushell fs check-file
+use ../../../.nushell plot [ into-axis-options, COMMON_OPTIONS, gplt ]
 
 export def main [data: path, --save: path] {
     check-file $data --span (metadata $data).span

benchmarks/.nushell/fec/plot.nu

-use ../../../.nushell/math.nu *
-use ../../../.nushell/plot.nu [ into-axis-options, COMMON_OPTIONS ]
-use ../../../.nushell/fs.nu check-file
-use ../../../.nushell/plot.nu gplt
+use ../../../.nushell math *
+use ../../../.nushell plot [ into-axis-options, COMMON_OPTIONS ]
+use ../../../.nushell fs check-file
+use ../../../.nushell plot gplt
 
 export def encoding [data: path, --save: path] {
     check-file $data --span (metadata $data).span

benchmarks/.nushell/fec/run.nu

-use ../../../.nushell/formats.nu *
+use ../../../.nushell formats *
 
 export def main [
     --output: path = "./fec.ndjson",

benchmarks/.nushell/recoding/plot.nu

-use ../../../.nushell/math.nu *
-use ../../../.nushell/plot.nu [ into-axis-options, COMMON_OPTIONS ]
-use ../../../.nushell/fs.nu check-file
-use ../../../.nushell/plot.nu gplt
+use ../../../.nushell math *
+use ../../../.nushell plot [ into-axis-options, COMMON_OPTIONS ]
+use ../../../.nushell fs check-file
+use ../../../.nushell plot gplt
 
 export def main [data: path, --save: path] {
     check-file $data --span (metadata $data).span

benchmarks/.nushell/recoding/run.nu

-use ../../../.nushell/formats.nu *
+use ../../../.nushell formats *
 
 export def main [
     --output: path = "./recoding.ndjson",

benchmarks/.nushell/setup/plot.nu

-use ../../../.nushell/math.nu *
-use ../../../.nushell/fs.nu check-file
-use ../../../.nushell/plot.nu [ into-axis-options, COMMON_OPTIONS, gplt ]
+use ../../../.nushell math *
+use ../../../.nushell fs check-file
+use ../../../.nushell plot [ into-axis-options, COMMON_OPTIONS, gplt ]
 
 export def main [data: path, --save: path] {
     check-file $data --span (metadata $data).span

bins/inbreeding/plot.nu

 use std repeat
 
 use consts.nu
-use ../../.nushell/plot.nu gplt
-use ../../.nushell/color.nu *
-use ../../.nushell/error.nu "error throw"
+use ../../.nushell plot gplt
+use ../../.nushell color *
+use ../../.nushell error "error throw"
 
 def "parse strategy" []: string -> record<type: string> {
     let s = $in

bins/inbreeding/run.nu

 use consts.nu
-use ../../.nushell/cargo.nu "cargo bin"
+use ../../.nushell cargo "cargo bin"
 
 export def main [
     --options: record<

examples/cli.nu

@@ -7,7 +7,7 @@ use ../komodo.nu [
     "komodo reconstruct",
     "komodo ls",
 ]
-use ../.nushell/binary.nu [ "bytes from_int" ]
+use ../.nushell binary [ "bytes from_int" ]
 
 use std assert
 

komodo.nu

@@ -2,7 +2,7 @@
 #
 # please run `komodo --help` or `komodo <tab>` to have a look at more information
 
-use .nushell/binary.nu ["bytes from_int"]
+use .nushell binary ["bytes from_int"]
 
 const KOMODO_BINARY = "./target/release/komodo"
 const DEFAULT_LOG_LEVEL = "INFO"

tests/binary.nu

-use ../.nushell/binary.nu [
+use ../.nushell binary [
     "bytes decode", "bytes encode", "bytes from_int", "bytes to_int"
 ]
 

tests/cli.nu

@@ -7,7 +7,7 @@ use ../komodo.nu [
     "komodo ls",
     "komodo clean",
 ]
-use ../.nushell/binary.nu [ "bytes from_int" ]
+use ../.nushell binary [ "bytes from_int" ]
 
 use std assert
 

tests/color.nu

-use ../.nushell/color.nu [
+use ../.nushell color [
     "color from-floats",
     "color from-ints",
     "color from-string",