fix: resolve embedding and clustering bugs for large repos

[thuongh2]

Summary

This PR fixes three critical bugs that affect large-scale repositories (100k+ symbols):

1. Embedding Worker Graceful Shutdown (#3)

Problem: The embedding worker started in a goroutine but the channel was never closed and analyze never waited for completion. The process exited before the worker could process even a single batch, leaving embeddings at 0%.

Fix:

• Added Close() method to Worker that closes the queue channel and waits via sync.WaitGroup
• analyze.go now calls w.Close() after enqueueing all jobs, blocking until embeddings complete

2. Embedding Queue Capacity (#4)

Problem: Queue buffer was only 1,000 jobs with silent drop on full. Repos with >1,000 symbols had embeddings silently dropped (e.g., 133k symbols → only 1,000 embedded).

Fix:

• Increased buffer from 1,000 to 100,000 jobs
• Added warning log when jobs are dropped: log.Printf("embedder: job dropped for %s (queue full)", job.UID)

3. SetClusterForNodes SQLite Variable Limit (#5)

Problem: SetClusterForNodes built a single WHERE uid IN (?, ?, ...) query with one placeholder per UID. SQLite has a ~999 variable limit, causing "too many SQL variables" error on clusters with >998 members.

Fix:

• Batch UIDs into chunks of 500
• Execute multiple UPDATE queries within the same transaction
• Follows the same pattern as UpsertClusterMembers

Testing

All existing tests pass:

$ go test ./...
ok    github.com/thuongh2/git-mimir/internal/cluster
ok    github.com/thuongh2/git-mimir/internal/daemon
ok    github.com/thuongh2/git-mimir/internal/incremental
ok    github.com/thuongh2/git-mimir/internal/parser
ok    github.com/thuongh2/git-mimir/internal/process
ok    github.com/thuongh2/git-mimir/internal/resolver
ok    github.com/thuongh2/git-mimir/internal/setup
ok    github.com/thuongh2/git-mimir/internal/store

Impact

• Repos with 100k+ symbols can now complete mimir analyze without errors
• All embeddings are generated before analyze exits
• No more silent job drops or SQLite variable limit crashes