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fix(#424): factor DB emptiness into default resolution; repair bootstrap.sh binary name (#425)
Follow-up to #421/#423. Purely path-based default-DB precedence let a stale, empty higher-precedence DB shadow a live lower-precedence one (the exact reported case: empty ~/.mimir/data/mimir.db chosen over a live ~/mimir.db). - resolve_default_db now takes a keyless entity-count probe. Only when the highest-precedence *existing* candidate is known-empty (Some(0)) does it prefer the highest-precedence known-non-empty candidate. Unknown candidates (locked/corrupt/not-yet-a-vault -> None) are never demoted-on nor promoted-to, so it degrades to the current path order + split-brain warning. - probe_entity_count opens candidates read-only (no schema init / WAL churn, unlike Database::open) and counts entities; a row COUNT needs no key since encryption is per-field. - Resolution + warnings centralized in normalize_default_db(), run once in main() before the command match, so serve and all maintenance subcommands open the same resolved DB (replaces the scattered check_legacy_db calls). default_db_path() (clap's eager default) stays path-only and side-effect-free. - 5 new unit tests cover the emptiness cases; the 5 existing #421 precedence tests updated to the new signature (unchanged assertions via an all-unknown probe). Full bin suite: 338 passed. - scripts/bootstrap.sh looked for target/release/mimir, which the perseus-vault crate no longer emits (build succeeded then failed to find the binary). Now builds/installs perseus-vault + mimir/mneme compat symlinks, defaults to perseus-vault.db, and uses the serve subcommand — matching install.sh. Co-authored-by: tcconnally <hermes@perseus.observer> Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
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‎CHANGELOG.md‎

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@@ -5,6 +5,27 @@ All notable changes to Perseus Vault (formerly Mimir/Mneme) are documented here.
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## [Unreleased]
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### Fixed
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- Default DB resolution now factors in emptiness (#424, follow-up to #421):
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when the database path is the implicit default (no `--db`, no
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`$MIMIR_DB_PATH`) and the highest-precedence candidate DB is *known-empty*
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(`SELECT COUNT(*) FROM entities == 0` — a keyless read, works under
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encryption), a lower-precedence but *non-empty* candidate is preferred
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instead. This fixes the reported case where a stale-empty
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`~/.mimir/data/mimir.db` shadowed a live `~/mimir.db`. Candidates that can't
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be read (locked/corrupt/not-yet-a-vault) are treated as unknown — never
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demoted-on and never promoted-to — so behavior degrades gracefully to the
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path-based order plus the existing split-brain warning. Resolution + its
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warnings are now performed once in `main()` (`normalize_default_db`), so
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`serve` and every maintenance subcommand open the same resolved DB
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(previously only a handful of sites warned). `default_db_path()` (clap's
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eager default) stays path-only and side-effect-free.
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- `scripts/bootstrap.sh` looked for a `target/release/mimir` binary that the
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`perseus-vault`-named crate no longer produces (the build would report
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success then fail to find the binary). It now builds/installs `perseus-vault`
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with `mimir`/`mneme` compat symlinks, defaults to `perseus-vault.db`, and
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uses the `serve` subcommand — matching `scripts/install.sh` (#424).
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### Added
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- History retention mechanism (#398): entity_history can now be bounded via
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env knobs — `MIMIR_HISTORY_MAX_AGE_DAYS`, `MIMIR_HISTORY_MAX_VERSIONS_PER_KEY`

‎scripts/bootstrap.sh‎

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@@ -1,20 +1,21 @@
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#!/usr/bin/env bash
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# =============================================================================
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# Mimir One-Shot Bootstrap
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# Perseus Vault One-Shot Bootstrap (build from source)
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# Persistent memory engine for AI agents — MCP JSON-RPC stdio server
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#
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# Usage:
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# curl -sSL https://raw.githubusercontent.com/Perseus-Computing-LLC/mimir/main/scripts/bootstrap.sh | bash
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# curl -sSL https://raw.githubusercontent.com/Perseus-Computing-LLC/perseus-vault/main/scripts/bootstrap.sh | bash
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#
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# What this does:
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# 1. Installs system dependencies (Rust toolchain via rustup, build tools)
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# 2. Clones and builds Mimir from source (release binary)
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# 3. Installs the binary to ~/.local/bin/mimir
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# 2. Clones and builds Perseus Vault from source (release binary)
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# 3. Installs the binary to ~/.local/bin/perseus-vault (+ mimir/mneme compat symlinks)
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# 4. Creates the data directory and generates .env defaults
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# 5. Verifies the installation and prints a success summary
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#
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# Idempotent — safe to re-run. Existing binary is only rebuilt if
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# FORCE=1 or the repo checkout is stale.
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# Prefer scripts/install.sh if you just want a prebuilt binary; this script is
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# for building from source. Idempotent — safe to re-run. Existing binary is
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# only rebuilt if FORCE=1 or the repo checkout is stale.
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# =============================================================================
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set -euo pipefail
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@@ -33,18 +34,23 @@ info() { printf "${CYAN}→${NC} %s\n" "$*"; }
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header() { printf "\n${BOLD}══ %s ══${NC}\n" "$*"; }
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FORCE="${FORCE:-0}"
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MIMIR_REPO="https://github.com/Perseus-Computing-LLC/mimir.git"
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# Repo redirects from the historical mimir/mneme names, but use the canonical
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# one so the clone URL matches what users see everywhere else.
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VAULT_REPO="https://github.com/Perseus-Computing-LLC/perseus-vault.git"
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# Script-local dirs. NOTE: MIMIR_DB_PATH is the *real* env var the binary reads
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# (see default_db_path() in src/main.rs), so it keeps its name for compatibility;
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# the default filename is the canonical perseus-vault.db.
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MIMIR_DIR="${MIMIR_DIR:-$HOME/.mimir}"
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MIMIR_BIN_DIR="${MIMIR_BIN_DIR:-$HOME/.local/bin}"
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MIMIR_DATA_DIR="${MIMIR_DATA_DIR:-$HOME/.mimir/data}"
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MIMIR_DB_PATH="${MIMIR_DB_PATH:-$MIMIR_DATA_DIR/mimir.db}"
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MIMIR_DB_PATH="${MIMIR_DB_PATH:-$MIMIR_DATA_DIR/perseus-vault.db}"
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WORKSPACE="${WORKSPACE:-$(pwd)}"
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echo ""
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echo "============================================"
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echo " Mimir One-Shot Bootstrap"
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echo " Perseus Vault One-Shot Bootstrap"
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echo " Persistent memory engine for AI agents"
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echo " github.com/Perseus-Computing-LLC/mimir"
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echo " github.com/Perseus-Computing-LLC/perseus-vault"
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echo "============================================"
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# ── Step 1: System dependencies ─────────────────────────────────────────────
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if command -v cc &>/dev/null; then
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ok "C compiler: $(cc --version 2>&1 | head -1)"
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else
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fail "C compiler is required to build Mimir (rusqlite with bundled SQLite). Install build-essential or equivalent."
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fail "C compiler is required to build Perseus Vault (rusqlite with bundled SQLite). Install build-essential or equivalent."
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fi
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# Check/install Rust
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fi
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fi
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# ── Step 2: Clone / update Mimir repo ───────────────────────────────────────
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header "Step 2: Clone & build Mimir"
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# ── Step 2: Clone / update repo ─────────────────────────────────────────────
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header "Step 2: Clone & build Perseus Vault"
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if [ -d "$MIMIR_DIR/.git" ]; then
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info "Updating existing checkout at $MIMIR_DIR..."
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ok "Repo is up to date"
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fi
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else
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info "Cloning Mimir from GitHub..."
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info "Cloning Perseus Vault from GitHub..."
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rm -rf "$MIMIR_DIR"
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git clone --depth 1 "$MIMIR_REPO" "$MIMIR_DIR"
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git clone --depth 1 "$VAULT_REPO" "$MIMIR_DIR"
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fi
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# Build release binary
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info "Building Mimir (release)..."
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# Build release binary. The crate/bin is named perseus-vault, so cargo emits
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# target/release/perseus-vault (this path was stale — it used to look for a
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# `mimir` binary that no longer exists, #424).
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info "Building Perseus Vault (release)..."
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cd "$MIMIR_DIR"
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cargo build --release 2>&1 | tail -5
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BINARY="$MIMIR_DIR/target/release/mimir"
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BINARY="$MIMIR_DIR/target/release/perseus-vault"
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if [ ! -f "$BINARY" ]; then
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fail "Build failed. Check the output above for errors."
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fail "Build failed (expected $BINARY). Check the output above for errors."
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fi
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ok "Binary built: $BINARY ($(du -h "$BINARY" | cut -f1))"
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# ── Step 3: Install binary ──────────────────────────────────────────────────
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header "Step 3: Install binary"
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mkdir -p "$MIMIR_BIN_DIR"
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cp "$BINARY" "$MIMIR_BIN_DIR/mimir"
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chmod +x "$MIMIR_BIN_DIR/mimir"
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cp "$BINARY" "$MIMIR_BIN_DIR/perseus-vault"
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chmod +x "$MIMIR_BIN_DIR/perseus-vault"
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# Backward-compatible names so existing configs referencing mimir/mneme keep
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# working (mirrors scripts/install.sh).
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ln -sf "$MIMIR_BIN_DIR/perseus-vault" "$MIMIR_BIN_DIR/mimir"
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ln -sf "$MIMIR_BIN_DIR/perseus-vault" "$MIMIR_BIN_DIR/mneme"
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# macOS Apple silicon: a freshly built (unsigned) binary is SIGKILLed on first
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# run — `mimir --version` prints "Killed: 9" with no other output (#422). Apply
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# an ad-hoc code signature so it launches. Guarded by Darwin + arm64 so it is a
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# no-op on Intel macOS and other platforms.
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# run — `perseus-vault --version` prints "Killed: 9" with no other output
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# (#422). Apply an ad-hoc code signature so it launches. Guarded by Darwin +
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# arm64 so it is a no-op on Intel macOS and other platforms.
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if [ "$(uname -s)" = "Darwin" ] && [ "$(uname -m)" = "arm64" ] && command -v codesign >/dev/null 2>&1; then
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info "Ad-hoc code-signing binary (macOS Apple silicon, #422)..."
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if codesign --force --sign - "$MIMIR_BIN_DIR/mimir" 2>/dev/null; then
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if codesign --force --sign - "$MIMIR_BIN_DIR/perseus-vault" 2>/dev/null; then
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ok "Ad-hoc code-signed"
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else
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warn "Could not code-sign. If 'mimir' is Killed: 9, run:"
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warn " codesign --force --sign - $MIMIR_BIN_DIR/mimir"
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warn "Could not code-sign. If 'perseus-vault' is Killed: 9, run:"
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warn " codesign --force --sign - $MIMIR_BIN_DIR/perseus-vault"
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fi
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fi
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@@ -186,12 +198,12 @@ case ":$PATH:" in
186198
*) export PATH="$MIMIR_BIN_DIR:$PATH" ;;
187199
esac
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if command -v mimir &>/dev/null; then
190-
MIMIR_VER=$(mimir --version 2>&1 || echo "unknown")
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ok "mimir installed to $MIMIR_BIN_DIR/mimir"
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ok "Version: $MIMIR_VER"
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if command -v perseus-vault &>/dev/null; then
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VAULT_VER=$(perseus-vault --version 2>&1 || echo "unknown")
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ok "perseus-vault installed to $MIMIR_BIN_DIR/perseus-vault"
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ok "Version: $VAULT_VER"
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else
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fail "mimir not found on PATH after install. Check $MIMIR_BIN_DIR"
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fail "perseus-vault not found on PATH after install. Check $MIMIR_BIN_DIR"
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fi
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# ── Step 4: Create data directory ───────────────────────────────────────────
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if [ ! -f "$MIMIR_DB_PATH" ]; then
210222
info "Warming up database at $MIMIR_DB_PATH..."
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# Brief serve+kill to trigger DB creation
212-
timeout 2 mimir --db "$MIMIR_DB_PATH" 2>/dev/null || true
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timeout 2 perseus-vault serve --db "$MIMIR_DB_PATH" 2>/dev/null || true
213225
if [ -f "$MIMIR_DB_PATH" ]; then
214226
ok "Database created: $MIMIR_DB_PATH"
215227
else
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223235
header "Step 5: Environment"
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225237
ENV_FILE="$WORKSPACE/.env"
226-
MIMIR_ENV_BLOCK="# ── Mimir ──────────────────────────────────────────────────────────────
238+
MIMIR_ENV_BLOCK="# ── Perseus Vault ──────────────────────────────────────────────────────
227239
# Database path (default shown)
228240
MIMIR_DB_PATH=$MIMIR_DB_PATH
229241
"
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240252
BOOTSTRAP_DATE=$(date -u +"%Y-%m-%dT%H:%M:%SZ" 2>/dev/null || date -u)
241253
cat > "$ENV_FILE" << ENVEOF
242254
# =============================================================================
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# Mimir Environment
244-
# Generated by Mimir bootstrap — ${BOOTSTRAP_DATE}
255+
# Perseus Vault Environment
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# Generated by Perseus Vault bootstrap — ${BOOTSTRAP_DATE}
245257
# =============================================================================
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# Database path
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259271
header "Step 6: Verify binary"
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261273
# Quick smoke test: start server directly, check it initializes
262-
SMOKE_OUT=$(timeout 2 mimir --db "$MIMIR_DB_PATH" 2>&1 </dev/null || true)
274+
SMOKE_OUT=$(timeout 2 perseus-vault serve --db "$MIMIR_DB_PATH" 2>&1 </dev/null || true)
263275
if echo "$SMOKE_OUT" | grep -q "MCP server ready"; then
264276
ok "MCP server initializes correctly"
265-
ok "Tools: mimir_recall, mimir_store, mimir_health"
277+
ok "Tools: perseus_vault_recall, perseus_vault_remember, perseus_vault_health"
266278
else
267279
warn "MCP smoke test had issues (non-critical). Manual check:"
268-
warn " Run: mimir --db $MIMIR_DB_PATH"
280+
warn " Run: perseus-vault serve --db $MIMIR_DB_PATH"
269281
fi
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271283
# ── Step 7: Success summary ─────────────────────────────────────────────────
272284
header "Success Summary"
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274286
echo ""
275-
printf " ${BOLD}%-30s${NC} %s\n" "Mimir version:" "$(mimir --version 2>&1 || echo 'unknown')"
276-
printf " ${BOLD}%-30s${NC} %s\n" "Binary:" "$MIMIR_BIN_DIR/mimir"
287+
printf " ${BOLD}%-30s${NC} %s\n" "Perseus Vault version:" "$(perseus-vault --version 2>&1 || echo 'unknown')"
288+
printf " ${BOLD}%-30s${NC} %s\n" "Binary:" "$MIMIR_BIN_DIR/perseus-vault"
277289
printf " ${BOLD}%-30s${NC} %s\n" "Database:" "$([ -f "$MIMIR_DB_PATH" ] && echo "✓ $MIMIR_DB_PATH" || echo 'created on first serve')"
278290
printf " ${BOLD}%-30s${NC} %s\n" "Data dir:" "$MIMIR_DATA_DIR"
279-
printf " ${BOLD}%-30s${NC} %s\n" "MCP tools:" "mimir_recall, mimir_store, mimir_health"
291+
printf " ${BOLD}%-30s${NC} %s\n" "MCP tools:" "perseus_vault_recall, perseus_vault_remember, perseus_vault_health"
280292
printf " ${BOLD}%-30s${NC} %s\n" "Cargo:" "$(cargo --version 2>&1)"
281293
printf " ${BOLD}%-30s${NC} %s\n" "OS:" "$(uname -s) $(uname -m)"
282294
printf " ${BOLD}%-30s${NC} %s\n" ".env:" "$([ -f "$ENV_FILE" ] && echo '✓ exists' || echo '✗ missing')"
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284296
echo ""
285297
echo "============================================"
286-
echo " ${GREEN}Mimir bootstrap complete!${NC}"
298+
echo " ${GREEN}Perseus Vault bootstrap complete!${NC}"
287299
echo ""
288300
echo " Quick commands:"
289-
echo " mimir --db $MIMIR_DB_PATH # Start MCP server"
290-
echo " mimir --version # Show version"
301+
echo " perseus-vault serve --db $MIMIR_DB_PATH # Start MCP server"
302+
echo " perseus-vault --version # Show version"
291303
echo ""
292-
echo " Standalone MCP server:"
293-
echo " mimir --db $MIMIR_DB_PATH"
294-
echo ""
295-
echo " Docs: https://github.com/Perseus-Computing-LLC/mimir"
304+
echo " Docs: https://github.com/Perseus-Computing-LLC/perseus-vault"
296305
echo "============================================"

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