c++ shell for linux

Formatting.

This is one large wall of text. You need to split things up into logical sections to make this easyier to read. Add some vertical space between section to make this easier to read.

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You have a bunch of #include. Its nice to order them. You can choose any way to order it as long as its logical and makes it easy for people to look through.

I do most specific to most general.

 #include "HeaderFileForThisSource.h"
 #include "HeaderFileForOtherClassesInThisProject"
 ...
 #include <C++ Librries>
 ...
 #include <C Librries>
 ...
 #include <Standard C++ Header Files>
 ..
 #include <C standard Libraries>
 ...

Others list them alphabetically.

Not sure what is best but some logic to the ordering would be nice.

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This is really hard to read. I can't see the function names in the sea of text.

std::vector<std::string> Split(std::string input, char delim);
void Execute(const char *command, char *arglist[]);
std::map<std::string, std::string> alias(std::string file);
bool BuiltInCom(const char *command, char *arglist[],int arglist_size);
char** conv(std::vector<std::string> source);
bool createAlias(std::string first, std::string sec);
std::string replaceAll(std::string data, std::map <std::string, std::string> dict);

With some judisious use of using and some tidying you can make that really easy to use.

using  Store = std::vector<std::string>;
using  Map   = std::map<std::string, std::string>;
using  CPPtr = char**;

Store       Split(std::string input, char delim);
void        Execute(const char *command, char *arglist[]);
Map         alias(std::string file);
bool        BuiltInCom(const char *command, char *arglist[],int arglist_size);
CPPtr       conv(std::vector<std::string> source);
bool        createAlias(std::string first, std::string sec);
std::string replaceAll(std::string data, std::map <std::string, std::string> dict);

Code

Global "Variables" are a bad idea.

std::string USERDIR = getenv("HOME");
std::string ALIASFILE = USERDIR+"/shell/.alias";

Set this up in main(). You can then either pass these around as parameters or add them to an object.

You can have static immutable state in the global scope. This is for things like constants.

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Make it easy to read.

  while (1) {

This would be better as:

  while(true) {

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Don't use fixed size buffers where the user could input arbitrary length strings. C++ has the std::string to handle this kind of situation.

    char path[100];
    getcwd(path, 100);

    // Rather
    std::string  path = std::filesystem::current_path().string();

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Don't use magic numbers in your code:

    char prompt[110] = "$[";

Why a 110? Put the magic numbers into named constants

    // Near the top of the programe with all other constants.
    // Then you can tune your program without having to search for the constants.
    static std::size_t constepxr bufferSize = 110;

    .....
    char buffer[bufferSize];

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Should be using std::string here

    strcat(prompt, path);
    strcat(prompt,"]: ");

The old C string functions are not safe.

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There are several improvements you can do for this code using just c++ standard library classes and functions.

1. Don't use #include <bits/stdc++.h>

It's not guaranteed that this header file exists, and is a compiler specific internal. Using such will make your code less portable.
Only #include headers provided for the classes and functions you want to use from the c++ standard library.
You can read more about the possible consequences and problems here: Why should I not #include <bits/stdc++.h>?

As well don't #include header files where you don't use anything from them (e.g. #include <filesystem>).

2. Don't use c library functions for string manipulations

E.g. your code to build the prompt variable can be drastically simplified by just using std::string instead of char*:

char path[100];
getcwd(path,100);
std::string prompt = "$[" + std::string(path) + "]:";

Also you can simply write

if(command == "quit"){

supposed you use const std::string& as type for the command parameter.

3. You don't need to allocate arrays of char* variables to pass them to execxy() functions

Just built a std::vector<const char*> instead of your conv() function:

void Execute(const std::string& command, const std::vector<std::string>& args) {
  std::vector<const char*> cargs;
  pid_t pid;

  for(auto sarg : args) {
      cargs.append(sarg.data());
  }
  cargs.append(nullptr);

  //Creates a new proccess
  if ((pid = fork()) < 0) {
    std::cout << "Error: Cannot create new process" << std::endl;
    exit(-1);
  } else if (pid == 0) {
    //Executes the command
    if (execvp(command.data(), cargs.data()) < 0) {
      std::cout << "Could not execute command" << std::endl;
      exit(-1);
    } else {
      sleep(2);
    }
  }
  //Waits for command to finish
  if (waitpid(pid, NULL, 0) != pid) {
    std::cout << "Error: waitpid()";
    exit(-1);
  }
}

In such case where you use raw data pointers obtained by e.g. std::string::data(), be sure that the lifetimes of the underlying variables last throughout their use in e.g. C library functions.

As a general rule of thumb:
Avoid doing memory management yourself using new and delete explicitely. Rather use a c++ standard container or at least smart pointers.

4. You don't need explicit comparison for bool values

Change

if(BuiltInCom(com, arglist, parsed_string.size()) == 0){

to

if(!BuiltInCom(com, arglist, parsed_string.size())){

Also use false and true instead of the implicit conversions from int 0 and 1 literals.

5. Use const and pass by reference for parameters whenever possible

Use const if you don't need to change the parameter.
Use pass by reference (&) if you want to avoid unnecessary copies made for non trivial types.

You can see how in the example of Execute() I've given above.

Same goes for example

std::string replaceAll(std::string data, std::map <std::string, std::string> dict);

this should be

std::string& replaceAll(std::string& data, const std::map <std::string, std::string>& dict);