Add positive include prefixes for semantic indexing

[2Obe]

What problem would this solve?

Semantic indexing currently supports a negative carve-out through OBSIDIAN_EMBED_EXCLUDE. This is convenient when most of a vault belongs in semantic retrieval.

Some vaults instead have a deliberately bounded knowledge corpus. For example:

Knowledge/
Sources/

while the rest of the vault contains working files, archives, scratch material, or other content that should never enter semantic retrieval.
This is the case e.g. if you want to have a "First Brain" which is used e.g. as a normal obsidian notebook as usual and you have another "Second Brain" which is fed by the first brain but both live in your Vault.

Maintaining exclusions for every non-retrieval folder is fragile because newly created folders become eligible automatically.

Proposed solution

Add an optional positive include-prefix configuration, for example:

 OBSIDIAN_EMBED_INCLUDE=Knowledge/,Sources/

Behavior:

• absent/empty → current behavior unchanged;
• present → only matching vault-relative prefixes are eligible;
• hardcoded safety exclusions still apply;
• OBSIDIAN_EMBED_EXCLUDE has precedence and can carve out subtrees;
• index coverage uses exactly the same eligibility function;
• cached entries that fall outside the current scope are removed on rebuild.

Suggested shared semantics:

def is_retrieval_eligible(path, include_prefixes, exclude_prefixes):
     if include_prefixes and not matches_any(path, include_prefixes):
         return False
     if matches_any(path, exclude_prefixes):
         return False
     return True

Backward compatibility

With no include prefixes configured, semantic indexing behaves exactly as it does today.

Acceptance criteria

• empty include list retains current behavior
• one or more include prefixes restrict indexing
• existing embed exclusions still override includes
• coverage and index builder use identical scope logic
• out-of-scope cached entries disappear after rebuild
• tests cover nested folders, prefix boundaries and Windows/POSIX path normalization

Non-goals

No changes to embeddings, chunking, ranking or retrieval fusion.