Respect `.gitignore` when indexing (skip `node_modules` etc.)

[sdserranog]

When indexing JS/TS projects, node_modules and other ignored directories get indexed unnecessarily, slowing things down and bloating the library.

Proposal:

• Skip files/directories matched by .gitignore by default
• Add a flag to libr add to opt out when needed (e.g. --include-ignored)

libr add ~/my-js-project                     # skips node_modules
libr add ~/my-js-project --include-ignored   # indexes everything