fix: applyConfigDefaults uses full port resolution chain

[mrmaxsteel]

Summary

applyConfigDefaults() in store.go only checked env vars (BEADS_DOLT_SERVER_PORT / BEADS_DOLT_PORT) for port resolution. When no env var was set, cfg.ServerPort stayed at 0, and the MySQL driver defaulted to port 3307. If another project's Dolt was running on 3307, bd connected to the wrong database — causing PROJECT IDENTITY MISMATCH errors.

The fix: when cfg.ServerPort is still 0 after env var check, call doltserver.DefaultConfig(cfg.Path) to resolve using the full priority chain (port file > config.yaml > metadata.json > ephemeral). This function already existed and was used by open.go — it just wasn't wired into applyConfigDefaults().

Fixes #2590

The bug

Two independent port resolution paths existed:

Path	Location	Reads port file?	Reads config.yaml?	Reads metadata.json?
doltserver.DefaultConfig()	doltserver.go:298	Yes	Yes	Yes
applyConfigDefaults()	store.go:545	No	No	No

applyConfigDefaults() is called by New() (the main store constructor). So every bd command that opens a store used the incomplete resolution path.

The fix

6 lines added after the env var check in applyConfigDefaults():

if cfg.ServerPort == 0 && cfg.Path != "" {
    if resolved := doltserver.DefaultConfig(cfg.Path); resolved.Port > 0 {
        cfg.ServerPort = resolved.Port
    }
}

Reproduction

Port file (.beads/dolt-server.port): 13958
metadata.json dolt_server_port:      13958
config.yaml dolt.port:               13958
Server on 13958:                     PID 79454 (correct)
Server on 3307:                      PID 61645 (another project)

# BEFORE fix:
bd list → connects to 3307 → PROJECT IDENTITY MISMATCH
BEADS_DOLT_PORT=13958 bd list → works

# AFTER fix:
bd list → connects to 13958 → works (no env var needed)

Test plan

• go build ./... compiles
• go test ./internal/storage/dolt/ -run TestApplyConfigDefaults — 5 existing tests pass
• Manual verification: bd list connects to port file port without env var override
• Tests for port file fallback in applyConfigDefaults (would appreciate reviewer input on test approach — doltserver.DefaultConfig reads from filesystem)

🤖 Generated with Claude Code

[ktoulgaridis]

All non-Embedded-Dolt checks pass (9/9). Embedded Dolt failures are systemic across all PRs and main. Clean 6-line fix wiring applyConfigDefaults() into the full port resolution chain (port file > config.yaml > metadata.json). Prevents cross-project connections when no env var is set. LGTM.

[garitar]

Thanks for pushing on this. While auditing #2590, I found a remaining CLI case that still fails even when applyConfigDefaults() is improved: if metadata.json sets dolt_data_dir outside .beads, bd list can derive the wrong config directory from filepath.Dir(dbPath), lose the repo-local metadata/port/database settings, and fall back to the wrong server.

I opened a focused follow-up PR here with a deterministic repro that fails on unpatched origin/main and passes with the fix: #2614

Your PR helped narrow the search area, so I wanted to cross-link the remaining case here rather than duplicate discussion. Thanks again for digging into this.