feat(api): migrate all tools to SDK adapter with dual-path support (v0.5.0-beta.0)

Migrate all 17 tools to use the nia-ai-ts SDK adapter with backward compatibility:

SDK Migration:
- nia-search: Uses sdk.search.universal/query/web/deep
- nia-research: Uses sdk.search.deep with oracle streaming
- nia-index: Uses sdk.sources.create
- nia-manage-resource: Uses sdk.sources.list/get/update/delete
- nia-context: Uses sdk.contexts.create/list/get/update/delete/semanticSearch
- nia-tracer: Uses sdk.tracer.createJob/streamJob
- nia-advisor: Uses sdk.advisor.ask
- nia-package-search: Uses sdk.packages.search
- nia-auto-subscribe: Uses sdk.dependencies.analyze/subscribe
- nia-read: Uses sdk.filesystem.read
- nia-write: Uses sdk.filesystem.write
- nia-grep: Uses sdk.filesystem.grep
- nia-explore: Uses sdk.filesystem.tree
- nia-mkdir: Uses sdk.filesystem.mkdir
- nia-mv: Uses sdk.filesystem.mv
- nia-rm: Uses sdk.filesystem.rm
- nia-e2e: Uses sdk.daemon.* methods
- source-resolver: Uses sdk.sources.resolve

Infrastructure:
- Extended SDK adapter with low-level HTTP methods (get/post/put/patch/delete)
- Added abort signal support to all filesystem methods
- Updated job-manager with SDK streaming support
- Removed NiaClient casts from index.ts tool registry

All 170 unit tests pass. Integration tests against live API expected to have some failures due to API contract evolution.