find -name \*.java | xargs find_bom

find_bom.c

#include <errno.h>
#include <unistd.h>
#include <stdio.h>
#include <string.h>

#define UTF8_BOM    "\xef\xbb\xbf"
#define UTF16BE_BOM "\xfe\xff"
#define UTF16LE_BOM "\xff\xfe"
#define UTF7_BOM    "\x2b\x2f\x76"

int match(const char* name, const char* bom, size_t bom_bytes, const char* filename, int lineno, const char* buffer)
{
  int istty = isatty(fileno(stdout));
  char* p;
  if((p = strstr(buffer, bom)) != NULL) {
    int pos = p - buffer;
    printf("%s:%d: %s BOM at column %d\n", filename, lineno, name, pos);
    printf("> %.*s%s%s\n", pos, buffer,
      istty ? "\033[1;33m[BOM]\033[0m" : "[BOM]",
      buffer + pos + bom_bytes);
  }
  return p != NULL;
}

int main(int ac, char** av)
{
  char buffer[4096];

  while(*++av != NULL) {
    char* filename = *av;

    FILE* fp = fopen(filename, "rb");
    if(fp == NULL) {
      perror(filename);
      continue;
    }

    int lineno = 1;
    while(fgets(buffer, sizeof buffer, fp) != NULL) {
      match("UTF-7", UTF7_BOM, 4, filename, lineno, buffer);
      match("UTF-8", UTF8_BOM, 3, filename, lineno, buffer);
      match("UTF-16 LE", UTF16LE_BOM, 2, filename, lineno, buffer);
      match("UTF-16 BE", UTF16BE_BOM, 2, filename, lineno, buffer);

      lineno++;
    }

    fclose(fp);
  }

  return 0;
}