Fix/spaces primitive atoms

[NatnaelTigistu]

What this PR does

1. Fixes add-atom dropping primitive values. Previously, spaces.pl strictly expected incoming atoms to be S-Expression lists ([Rel|Args]). Adding a scalar primitive (like 42 or "Hello") would silently fail unification and be dropped. This PR wraps non-list atoms using an internal #primitive marker when asserting them to the Prolog database, and unwraps them during get-atoms and match operations.
2. Cleans up .gitignore. Replaced the specific __pycache__ directory rules with a global __pycache__/ rule, and ignored the dynamically generated repos/ folder to keep untracked files clean.

Changes

• src/spaces.pl: Added list-checking in add_sexp, remove_sexp, and match, ensuring primitives are safely stored and queried.
• .gitignore: Globalized __pycache__ and added repos/.
• Added examples/test_add_primitive.metta to the automated test suite to prevent regressions.

Testing

• Primitives (42, "Hello", true) are now successfully added and returned from !(match &space $x $x).
• Verified that all existing tests in sh test.sh continue to pass without regressions.