Merge remote session logs

15/26810bf9c1/0/content_hash.txt

@@ -0,0 +1 @@
+sha256:a9b5a1b4f23d30a8266524cf397682b8fc8e155606b43d2dca29be961e51f7af

15/26810bf9c1/0/context.md

@@ -0,0 +1,18 @@
+# Session Context
+
+## User Prompts
+
+### Prompt 1
+
+Implement the following plan:
+
+# Make SQLite Memory Limits Configurable via config.json
+
+## Context
+
+Fixes 1-4 for the SQLite memory leak are already implemented on this branch. The hardcoded defaults (200MB cache per connection, 1GB soft heap limit) are conservative. On the production server with 512GB RAM, these could be tuned higher for better query performance. Additionally, `RepositoryConfig` and `SetConfig()` exist but are **never wired up** — there's currently no way to override any re...
+
+### Prompt 2
+
+Also add a section in the README.md discussing and documenting the new db options.
+

15/26810bf9c1/0/metadata.json

@@ -0,0 +1,30 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "1526810bf9c1",
+  "session_id": "50b2b10a-1be0-441f-aafb-3c5828f0fcc9",
+  "strategy": "manual-commit",
+  "created_at": "2026-03-11T05:21:50.041031Z",
+  "branch": "optimize-db-indices",
+  "checkpoints_count": 2,
+  "files_touched": [
+    "README.md"
+  ],
+  "agent": "Claude Code",
+  "turn_id": "0dae2aa2a939",
+  "token_usage": {
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+    "cache_creation_tokens": 60054,
+    "cache_read_tokens": 488339,
+    "output_tokens": 4643,
+    "api_call_count": 16
+  },
+  "initial_attribution": {
+    "calculated_at": "2026-03-11T05:21:49.955788Z",
+    "agent_lines": 65,
+    "human_added": 0,
+    "human_modified": 0,
+    "human_removed": 0,
+    "total_committed": 65,
+    "agent_percentage": 100
+  }
+}

15/26810bf9c1/0/prompt.txt

@@ -0,0 +1,192 @@
+Implement the following plan:
+
+# Make SQLite Memory Limits Configurable via config.json
+
+## Context
+
+Fixes 1-4 for the SQLite memory leak are already implemented on this branch. The hardcoded defaults (200MB cache per connection, 1GB soft heap limit) are conservative. On the production server with 512GB RAM, these could be tuned higher for better query performance. Additionally, `RepositoryConfig` and `SetConfig()` exist but are **never wired up** — there's currently no way to override any repository defaults from config.json.
+
+## Current State (already implemented on this branch)
+
+- `_cache_size = -200000` (200MB per connection, hardcoded) — **too low for 80GB DB, will be made configurable**
+- `soft_heap_limit = 1073741824` (1GB process-wide, hardcoded) — **too low, will be made configurable**
+- `ConnectionMaxIdleTime = 10 * time.Minute` (hardcoded default)
+- `MaxOpenConnections = 4` (hardcoded default)
+- Context propagation to all query call sites (already done)
+
+## Problem
+
+`repository.SetConfig()` exists but is never called from `main.go`. The `initDatabase()` function (line 110) just calls `repository.Connect(config.Keys.DB)` directly. There's no `"db-config"` section in `ProgramConfig` or the JSON schema.
+
+## Proposed Changes
+
+### 1. Add SQLite memory fields to `RepositoryConfig`
+
+**File:** `internal/repository/config.go`
+
+Add two new fields with sensible defaults:
+
+```go
+type RepositoryConfig struct {
+    // ... existing fields ...
+
+    // DbCacheSizeMB is the SQLite page cache size per connection in MB.
+    // Uses negative PRAGMA cache_size notation (KiB). With MaxOpenConnections=4
+    // and DbCacheSizeMB=200, total page cache is up to 800MB.
+    // Default: 200 (MB)
+    DbCacheSizeMB int
+
+    // DbSoftHeapLimitMB is the process-wide SQLite soft heap limit in MB.
+    // SQLite will try to release cache pages to stay under this limit.
+    // It's a soft limit — queries won't fail, but cache eviction becomes more aggressive.
+    // Default: 1024 (1GB)
+    DbSoftHeapLimitMB int
+}
+```
+
+Update `DefaultConfig()`:
+```go
+DbCacheSizeMB:     2048,  // 2GB per connection
+DbSoftHeapLimitMB: 16384, // 16GB process-wide
+```
+
+**Rationale for defaults:** With an 80GB production database on a 512GB server, we want the cache to hold a significant portion of the DB. At 4 connections × 2GB = 8GB default page cache, plus 16GB soft heap limit. The previous 200MB/1GB hardcoded values were too conservative and would hurt query performance by forcing excessive cache eviction. These defaults use ~5% of a 512GB server — still safe for smaller machines, while enabling good performance on production.
+
+### 2. Use config values in `Connect()` and `setupSqlite()`
+
+**File:** `internal/repository/dbConnection.go`
+
+In `Connect()`, replace the hardcoded cache_size:
+```go
+cacheSizeKiB := repoConfig.DbCacheSizeMB * 1024  // Convert MB to KiB
+connectionURLParams.Add("_cache_size", fmt.Sprintf("-%d", cacheSizeKiB))
+```
+
+Change `setupSqlite()` to accept the config and use it for soft_heap_limit:
+```go
+func setupSqlite(db *sql.DB, cfg *RepositoryConfig) error {
+    pragmas := []string{
+        "temp_store = memory",
+        fmt.Sprintf("soft_heap_limit = %d", cfg.DbSoftHeapLimitMB*1024*1024),
+    }
+    // ...
+}
+```
+
+Update the call site in `Connect()`:
+```go
+err = setupSqlite(dbHandle.DB, &opts)  // was: setupSqlite(dbHandle.DB)
+```
+
+### 3. Add `"db-config"` section to `ProgramConfig` and JSON schema
+
+**File:** `internal/config/config.go`
+
+Add a new struct and field to `ProgramConfig`:
+
+```go
+type DbConfig struct {
+    CacheSizeMB       int `json:"cache-size-mb"`
+    SoftHeapLimitMB   int `json:"soft-heap-limit-mb"`
+    MaxOpenConnections int `json:"max-open-connections"`
+    MaxIdleConnections int `json:"max-idle-connections"`
+    ConnectionMaxIdleTimeMins int `json:"max-idle-time-minutes"`
+}
+
+type ProgramConfig struct {
+    // ... existing fields ...
+    DbConfig *DbConfig `json:"db-config"`
+}
+```
+
+**File:** `internal/config/schema.go`
+
+Add the schema section for validation.
+
+### 4. Wire `SetConfig()` in `initDatabase()`
+
+**File:** `cmd/cc-backend/main.go`
+
+```go
+func initDatabase() error {
+    if config.Keys.DbConfig != nil {
+        cfg := repository.DefaultConfig()
+        dc := config.Keys.DbConfig
+        if dc.CacheSizeMB > 0 {
+            cfg.DbCacheSizeMB = dc.CacheSizeMB
+        }
+        if dc.SoftHeapLimitMB > 0 {
+            cfg.DbSoftHeapLimitMB = dc.SoftHeapLimitMB
+        }
+        if dc.MaxOpenConnections > 0 {
+            cfg.MaxOpenConnections = dc.MaxOpenConnections
+        }
+        if dc.MaxIdleConnections > 0 {
+            cfg.MaxIdleConnections = dc.MaxIdleConnections
+        }
+        if dc.ConnectionMaxIdleTimeMins > 0 {
+            cfg.ConnectionMaxIdleTime = time.Duration(dc.ConnectionMaxIdleTimeMins) * time.Minute
+        }
+        repository.SetConfig(cfg)
+    }
+    repository.Connect(config.Keys.DB)
+    return nil
+}
+```
+
+### 5. Log effective values on startup
+
+**File:** `internal/repository/dbConnection.go`
+
+After setting PRAGMAs, log the effective values so operators can verify:
+```go
+cclog.Infof("SQLite config: cache_size=%dMB/conn, soft_heap_limit=%dMB, max_conns=%d",
+    repoConfig.DbCacheSizeMB, repoConfig.DbSoftHeapLimitMB, repoConfig.MaxOpenConnections)
+```
+
+## Example config.json (for 512GB server with 80GB database)
+
+```json
+{
+  "main": {
+    "db": "./var/job.db",
+    "db-config": {
+      "cache-size-mb": 16384,
+      "soft-heap-limit-mb": 131072,
+      "max-open-connections": 8,
+      "max-idle-time-minutes": 30
+    }
+  }
+}
+```
+
+This would give: 8 connections × 16GB cache = 128GB max page cache, with a 128GB soft heap limit. The entire 80GB database can be cached in memory. On a 512GB server that's ~25% of RAM.
+
+**Sizing guidance (for documentation):**
+- `cache-size-mb`: Set to `DB_size / max-open-connections` to allow the entire DB to be cached. E.g., 80GB DB with 8 connections → 10GB per connection minimum.
+- `soft-heap-limit-mb`: Set to total desired SQLite memory budget. Should be ≥ `cache-size-mb × max-open-connections` to avoid cache thrashing.
+
+## Files to Modify
+
+| File | Changes |
+|------|---------|
+| `internal/repository/config.go` | Add `DbCacheSizeMB`, `DbSoftHeapLimitMB` fields + defaults |
+| `internal/repository/dbConnection.go` | Use config values instead of hardcoded; pass config to `setupSqlite`; add startup log |
+| `internal/config/config.go` | Add `DbConfig` struct and field to `ProgramConfig` |
+| `internal/config/schema.go` | Add `"db-config"` JSON schema section |
+| `cmd/cc-backend/main.go` | Wire `SetConfig()` in `initDatabase()` |
+
+## Verification
+
+1. `go build ./...` — compiles
+2. `go test ./internal/repository/... ./internal/config/...` — tests pass
+3. Without `db-config` in config.json: defaults apply (200MB cache, 1GB heap) — backwards compatible
+4. With `db-config`: verify with `PRAGMA cache_size;` and `PRAGMA soft_heap_limit;` in sqlite3 CLI
+5. Check startup log shows effective values
+
+
+If you need specific details from before exiting plan mode (like exact code snippets, error messages, or content you generated), read the full transcript at: /Users/jan/.claude/projects/-Users-jan-prg-CC-cc-backend/520afa6a-6a70-437b-96c1-35c40ed3ec48.jsonl
+
+---
+
+Also add a section in the README.md discussing and documenting the new db options.

15/26810bf9c1/metadata.json

@@ -0,0 +1,26 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "1526810bf9c1",
+  "strategy": "manual-commit",
+  "branch": "optimize-db-indices",
+  "checkpoints_count": 2,
+  "files_touched": [
+    "README.md"
+  ],
+  "sessions": [
+    {
+      "metadata": "/15/26810bf9c1/0/metadata.json",
+      "transcript": "/15/26810bf9c1/0/full.jsonl",
+      "context": "/15/26810bf9c1/0/context.md",
+      "content_hash": "/15/26810bf9c1/0/content_hash.txt",
+      "prompt": "/15/26810bf9c1/0/prompt.txt"
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+    "api_call_count": 16
+  }
+}

af/7afc9a29ff/0/content_hash.txt

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+sha256:2acb0c920c03e15d278d2ceab4ca80e35ae17c4c587ab7ee35844144cac5e341

af/7afc9a29ff/0/context.md

@@ -0,0 +1,16 @@
+# Session Context
+
+## User Prompts
+
+### Prompt 1
+
+Implement the following plan:
+
+# Optimize Job Table Indexes for 20M Row Production Database
+
+## Context
+
+The `job` table has **79 indexes** (created in migrations 08/09), causing:
+1. **Wrong index selection** — without `ANALYZE` statistics, SQLite picks wrong indexes (e.g., `jobs_jobstate_energy` instead of `jobs_starttime` for ORDER BY queries), causing full-table temp B-tree sorts on 20M rows → timeouts
+2. **Excessive disk/memory overhead** — each index costs ~200-400MB at 20M rows; 79 inde...
+

af/7afc9a29ff/0/metadata.json

@@ -0,0 +1,32 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "af7afc9a29ff",
+  "session_id": "c31c699a-f492-48f7-bcf0-35d3ceeac243",
+  "strategy": "manual-commit",
+  "created_at": "2026-03-11T04:46:04.68213Z",
+  "branch": "optimize-db-indices",
+  "checkpoints_count": 1,
+  "files_touched": [
+    "internal/repository/migration.go",
+    "internal/repository/migrations/sqlite3/11_optimize-indexes.down.sql",
+    "internal/repository/migrations/sqlite3/11_optimize-indexes.up.sql"
+  ],
+  "agent": "Claude Code",
+  "turn_id": "93c57808e96c",
+  "token_usage": {
+    "input_tokens": 9,
+    "cache_creation_tokens": 28556,
+    "cache_read_tokens": 187757,
+    "output_tokens": 8980,
+    "api_call_count": 7
+  },
+  "initial_attribution": {
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+    "human_modified": 0,
+    "human_removed": 0,
+    "total_committed": 551,
+    "agent_percentage": 69.87295825771325
+  }
+}

af/7afc9a29ff/0/prompt.txt

@@ -0,0 +1,139 @@
+Implement the following plan:
+
+# Optimize Job Table Indexes for 20M Row Production Database
+
+## Context
+
+The `job` table has **79 indexes** (created in migrations 08/09), causing:
+1. **Wrong index selection** — without `ANALYZE` statistics, SQLite picks wrong indexes (e.g., `jobs_jobstate_energy` instead of `jobs_starttime` for ORDER BY queries), causing full-table temp B-tree sorts on 20M rows → timeouts
+2. **Excessive disk/memory overhead** — each index costs ~200-400MB at 20M rows; 79 indexes = ~16-32GB wasted
+3. **Slower writes** — every INSERT/UPDATE touches all 79 indexes
+4. **Planner confusion** — too many similar indexes make the query planner's cost estimation unreliable
+
+The `ANALYZE` fix (already added to `setupSqlite` in `dbConnection.go`) resolves the planner issue with current indexes, but the index count must be reduced for disk/write performance.
+
+## Approach: Reduce to 20 indexes
+
+The key insight from query plan analysis: with `ANALYZE` and `LIMIT`, a `(filter_col, sort_col)` index is often better than `(filter_col1, filter_col2, sort_col)` because SQLite can scan the index in sort order and cheaply filter non-matching rows, stopping at LIMIT.
+
+### Verified query plans (with ANALYZE, after this change)
+
+| # | Pattern | Index Used | Plan |
+|---|---------|-----------|------|
+| 1 | Multi-state IN + ORDER BY start_time LIMIT | `jobs_starttime` | SCAN (index order, no sort) |
+| 2 | cluster + state + sort start_time | `jobs_cluster_starttime_duration` | SEARCH |
+| 3 | hpc_user + sort start_time | `jobs_user_starttime_duration` | SEARCH |
+| 4 | cluster + state aggregation | `jobs_cluster_jobstate_duration_starttime` | COVERING SEARCH |
+| 5 | Unique lookup (job_id,cluster,start_time) | `sqlite_autoindex_job_1` | SEARCH |
+| 6 | Running jobs for cluster + duration > | `jobs_cluster_jobstate_duration_starttime` | SEARCH |
+| 7 | start_time BETWEEN range | `jobs_starttime` | SEARCH |
+| 8 | GROUP BY user with cluster | `jobs_cluster_user` | COVERING SEARCH |
+| 9 | Concurrent jobs (cluster + start_time <) | `jobs_cluster_starttime_duration` | SEARCH |
+| 10 | project IN + state IN + sort | `jobs_jobstate_project` | SEARCH + temp sort |
+| 11 | user + multi-state + sort start_time | `jobs_user_starttime_duration` | SEARCH |
+| 12 | cluster + state + sort duration | `jobs_cluster_jobstate_duration_starttime` | SEARCH |
+| 13 | cluster + state + sort num_nodes | `jobs_cluster_numnodes` | SEARCH (state filtered per-row) |
+| 14 | Tag join | `tags_tagid` + PK | SEARCH |
+| 15 | Delete before timestamp | `jobs_starttime` | COVERING SEARCH |
+| 16 | Non-running jobs (GetJobList) | `jobs_jobstate_duration_starttime` | COVERING SCAN |
+
+## Changes Required
+
+### File: `internal/repository/migrations/sqlite3/11_optimize-indexes.up.sql` (new)
+
+```sql
+-- Drop all 77 job indexes from migration 09 (sqlite_autoindex_job_1 is UNIQUE, kept)
+-- Then create optimized set of 20
+
+-- GROUP 1: Global (1 index)
+-- #1 jobs_starttime (start_time)
+--    Default sort for unfiltered/multi-state queries, time range, delete-before
+
+-- GROUP 2: Cluster-prefixed (8 indexes)
+-- #2 jobs_cluster_starttime_duration (cluster, start_time, duration)
+--    Cluster + default sort, concurrent jobs, time range within cluster
+-- #3 jobs_cluster_duration_starttime (cluster, duration, start_time)
+--    Cluster + sort by duration
+-- #4 jobs_cluster_jobstate_duration_starttime (cluster, job_state, duration, start_time)
+--    COVERING for cluster+state aggregation; running jobs (cluster, state, duration>?)
+-- #5 jobs_cluster_jobstate_starttime_duration (cluster, job_state, start_time, duration)
+--    Cluster+state+sort start_time (single state equality)
+-- #6 jobs_cluster_user (cluster, hpc_user)
+--    COVERING for GROUP BY user with cluster filter
+-- #7 jobs_cluster_project (cluster, project)
+--    GROUP BY project with cluster filter
+-- #8 jobs_cluster_subcluster (cluster, subcluster)
+--    GROUP BY subcluster with cluster filter
+-- #9 jobs_cluster_numnodes (cluster, num_nodes)
+--    Cluster + sort by num_nodes (state filtered per-row, fast with LIMIT)
+
+-- GROUP 3: User-prefixed (1 index)
+-- #10 jobs_user_starttime_duration (hpc_user, start_time, duration)
+--     Security filter (user role) + default sort
+
+-- GROUP 4: Project-prefixed (1 index)
+-- #11 jobs_project_starttime_duration (project, start_time, duration)
+--     Security filter (manager role) + default sort
+
+-- GROUP 5: JobState-prefixed (3 indexes)
+-- #12 jobs_jobstate_project (job_state, project)
+--     State + project filter (for manager security within state query)
+-- #13 jobs_jobstate_user (job_state, hpc_user)
+--     State + user filter/aggregation
+-- #14 jobs_jobstate_duration_starttime (job_state, duration, start_time)
+--     COVERING for non-running jobs scan, state + sort duration
+
+-- GROUP 6: Rare filters (1 index)
+-- #15 jobs_arrayjobid (array_job_id)
+--     Array job lookup (rare but must be indexed)
+
+-- GROUP 7: Secondary sort columns (5 indexes)
+-- #16 jobs_cluster_numhwthreads (cluster, num_hwthreads)
+-- #17 jobs_cluster_numacc (cluster, num_acc)
+-- #18 jobs_cluster_energy (cluster, energy)
+-- #19 jobs_cluster_partition_starttime (cluster, cluster_partition, start_time)
+--     Cluster+partition + sort start_time
+-- #20 jobs_cluster_partition_jobstate (cluster, cluster_partition, job_state)
+--     Cluster+partition+state filter
+```
+
+### What's dropped and why (59 indexes removed)
+
+| Category | Count | Why redundant |
+|----------|-------|---------------|
+| cluster+partition sort/filter variants | 8 | Kept only 2 partition indexes (#19, #20); rest use cluster indexes + row filter |
+| cluster+shared (all) | 8 | `shared` is rare; cluster index + row filter is fast |
+| shared-prefixed (all) | 8 | `shared` alone is never a leading filter |
+| cluster+jobstate sort variants (numnodes, hwthreads, acc, energy) | 4 | Replaced by `(cluster, sort_col)` indexes which work for any state combo with LIMIT |
+| user sort variants (numnodes, hwthreads, acc, energy, duration) | 5 | User result sets are small; temp sort is fast |
+| project sort variants + project_user | 6 | Same reasoning as user |
+| jobstate sort variants (numnodes, hwthreads, acc, energy) | 4 | State has low cardinality; cluster+sort indexes handle these |
+| single-filter+starttime (5) + single-filter+duration (5) | 10 | Queries always have cluster/user/project filter; standalone rare |
+| standalone duration | 1 | Covered by cluster_duration_starttime |
+| duplicate arrayjob variants | 1 | Simplified to single-column (array_job_id) |
+| redundant cluster_starttime variants | 2 | Consolidated into 2 cluster+time indexes |
+| cluster_jobstate_user, cluster_jobstate_project | 2 | Covered by cluster_user/cluster_project + state row filter |
+
+### File: `internal/repository/migrations/sqlite3/11_optimize-indexes.down.sql` (new)
+
+Recreate all 77 indexes from migration 09 for safe rollback.
+
+### File: `internal/repository/migration.go`
+
+Increment `Version` from `10` to `11`.
+
+## Verification
+
+1. `go build ./...` — compiles
+2. `go test ./internal/repository/...` — tests pass
+3. `cc-backend -migrate-db` on a test copy of production DB
+4. After migration, run `ANALYZE;` then verify all 16 query plans match the table above using:
+   ```sql
+   EXPLAIN QUERY PLAN SELECT * FROM job WHERE job.job_state IN ('completed','running','failed') ORDER BY job.start_time DESC LIMIT 50;
+   -- Should show: SCAN job USING INDEX jobs_starttime
+   ```
+5. Verify index count: `SELECT COUNT(*) FROM sqlite_master WHERE type='index' AND tbl_name='job';` → should be 21 (20 + autoindex)
+6. Compare DB file size before/after (expect ~70% reduction in index overhead)
+
+
+If you need specific details from before exiting plan mode (like exact code snippets, error messages, or content you generated), read the full transcript at: /Users/jan/.claude/projects/-Users-jan-prg-CC-cc-backend/42401d2e-7d1c-4c0e-abe6-356cb2d48747.jsonl

af/7afc9a29ff/metadata.json

@@ -0,0 +1,28 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "af7afc9a29ff",
+  "strategy": "manual-commit",
+  "branch": "optimize-db-indices",
+  "checkpoints_count": 1,
+  "files_touched": [
+    "internal/repository/migration.go",
+    "internal/repository/migrations/sqlite3/11_optimize-indexes.down.sql",
+    "internal/repository/migrations/sqlite3/11_optimize-indexes.up.sql"
+  ],
+  "sessions": [
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+      "transcript": "/af/7afc9a29ff/0/full.jsonl",
+      "context": "/af/7afc9a29ff/0/context.md",
+      "content_hash": "/af/7afc9a29ff/0/content_hash.txt",
+      "prompt": "/af/7afc9a29ff/0/prompt.txt"
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+    "output_tokens": 8980,
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+  }
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dd/d4fa4a7bbb/0/content_hash.txt

@@ -0,0 +1 @@
+sha256:baa496432701c4b8869f1ec775d7d28549cb708c7bf54dcbf42c158de11391ad

dd/d4fa4a7bbb/0/context.md

@@ -0,0 +1,18 @@
+# Session Context
+
+## User Prompts
+
+### Prompt 1
+
+Implement the following plan:
+
+# Fix Missing `rows.Close()` Memory Leaks in SQLite3 Queries
+
+## Context
+
+Production memory leaks traced to queries that do full table scans (e.g., job state list sorted by `start_time` on all jobs). The root cause is `sql.Rows` objects not being closed after query execution. In Go's `database/sql`, every `rows` returned by `.Query()` holds a database connection and associated buffers until `rows.Close()` is called. Without `defer rows.Close()`, these leak on ev...
+
+### Prompt 2
+
+Check if the fixes are correctly merged in nodes.go
+

dd/d4fa4a7bbb/0/metadata.json

@@ -0,0 +1,30 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "ddd4fa4a7bbb",
+  "session_id": "42401d2e-7d1c-4c0e-abe6-356cb2d48747",
+  "strategy": "manual-commit",
+  "created_at": "2026-03-11T04:09:43.830973Z",
+  "branch": "hotfix",
+  "checkpoints_count": 2,
+  "files_touched": [
+    "internal/repository/node.go"
+  ],
+  "agent": "Claude Code",
+  "turn_id": "8927e4f0c7b0",
+  "token_usage": {
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+    "human_modified": 0,
+    "human_removed": 0,
+    "total_committed": 550,
+    "agent_percentage": 4.545454545454546
+  }
+}

dd/d4fa4a7bbb/0/prompt.txt

@@ -0,0 +1,97 @@
+Implement the following plan:
+
+# Fix Missing `rows.Close()` Memory Leaks in SQLite3 Queries
+
+## Context
+
+Production memory leaks traced to queries that do full table scans (e.g., job state list sorted by `start_time` on all jobs). The root cause is `sql.Rows` objects not being closed after query execution. In Go's `database/sql`, every `rows` returned by `.Query()` holds a database connection and associated buffers until `rows.Close()` is called. Without `defer rows.Close()`, these leak on every code path (both success and error returns).
+
+## Findings
+
+**22 total `.Query()` calls** across the repository layer. **15 have `defer rows.Close()`**. **7 do not** (listed below). Additionally, 1 `Queryx` call in `tags.go` is also missing close.
+
+In `node.go`, `QueryNodes` and `QueryNodesWithMeta` have partial `rows.Close()` only in error paths but **not on the success path** and not via `defer`.
+
+`CountStates` and `CountStatesTimed` in `node.go` also lack `defer rows.Close()` (same partial pattern as above for CountStates, none at all for CountStatesTimed).
+
+## Changes Required
+
+### 1. `internal/repository/stats.go` — 6 functions missing `defer rows.Close()`
+
+Add `defer rows.Close()` immediately after the `if err != nil` check for each:
+
+| Line | Function |
+|------|----------|
+| 233 | `JobsStatsGrouped` |
+| 438 | `JobCountGrouped` |
+| 494 | `AddJobCountGrouped` |
+| 553 | `AddJobCount` |
+| 753 | `jobsStatisticsHistogram` |
+| 821 | `jobsDurationStatisticsHistogram` |
+| 946 | `jobsMetricStatisticsHistogram` |
+
+Pattern — after each `Query()` error check, add:
+```go
+rows, err := query.RunWith(r.DB).Query()
+if err != nil {
+    ...
+    return nil, err
+}
+defer rows.Close()   // <-- ADD THIS
+```
+
+### 2. `internal/repository/tags.go` — 2 leaks in `CountTags()`
+
+**Line 282**: `xrows` from `r.DB.Queryx(...)` — add `defer xrows.Close()` after error check.
+
+**Line 333**: `rows` from `q.RunWith(r.stmtCache).Query()` — add `defer rows.Close()` after error check.
+
+### 3. `internal/repository/tags.go` — 3 leaks in `GetTags`, `GetTagsDirect`, `getArchiveTags`
+
+**Line 508** (`GetTags`): add `defer rows.Close()` after error check.
+**Line 541** (`GetTagsDirect`): add `defer rows.Close()` after error check.
+**Line 579** (`getArchiveTags`): add `defer rows.Close()` after error check.
+
+### 4. `internal/repository/node.go` — 4 functions missing `defer rows.Close()`
+
+**Line 363** (`QueryNodes`): Replace the manual `rows.Close()` in the error path with `defer rows.Close()` immediately after the error check. Remove the explicit `rows.Close()` call on line 375.
+
+**Line 412** (`QueryNodesWithMeta`): Same pattern — add `defer rows.Close()` after error check, remove explicit `rows.Close()` on line 427.
+
+**Line 558** (`CountStates`): Add `defer rows.Close()` after error check. Remove explicit `rows.Close()` on line 569.
+
+**Line 620** (`CountStatesTimed`): Add `defer rows.Close()` after error check. Remove explicit `rows.Close()` on line 633.
+
+## Summary of All Edits
+
+| File | Function | Action |
+|------|----------|--------|
+| `stats.go:237` | `JobsStatsGrouped` | Add `defer rows.Close()` |
+| `stats.go:442` | `JobCountGrouped` | Add `defer rows.Close()` |
+| `stats.go:498` | `AddJobCountGrouped` | Add `defer rows.Close()` |
+| `stats.go:557` | `AddJobCount` | Add `defer rows.Close()` |
+| `stats.go:757` | `jobsStatisticsHistogram` | Add `defer rows.Close()` |
+| `stats.go:825` | `jobsDurationStatisticsHistogram` | Add `defer rows.Close()` |
+| `stats.go:950` | `jobsMetricStatisticsHistogram` | Add `defer rows.Close()` |
+| `tags.go:284` | `CountTags` (xrows) | Add `defer xrows.Close()` |
+| `tags.go:336` | `CountTags` (rows) | Add `defer rows.Close()` |
+| `tags.go:513` | `GetTags` | Add `defer rows.Close()` |
+| `tags.go:546` | `GetTagsDirect` | Add `defer rows.Close()` |
+| `tags.go:584` | `getArchiveTags` | Add `defer rows.Close()` |
+| `node.go:368` | `QueryNodes` | Add `defer rows.Close()`, remove manual close on L375 |
+| `node.go:417` | `QueryNodesWithMeta` | Add `defer rows.Close()`, remove manual close on L427 |
+| `node.go:563` | `CountStates` | Add `defer rows.Close()`, remove manual close on L569 |
+| `node.go:625` | `CountStatesTimed` | Add `defer rows.Close()`, remove manual close on L633 |
+
+## Verification
+
+1. `go build ./...` — ensure it compiles
+2. `go test ./internal/repository/...` — run repository tests
+3. `go vet ./internal/repository/...` — static analysis
+
+
+If you need specific details from before exiting plan mode (like exact code snippets, error messages, or content you generated), read the full transcript at: /Users/jan/.claude/projects/-Users-jan-prg-CC-cc-backend/28147033-ddc8-4056-b064-e0558fbc614e.jsonl
+
+---
+
+Check if the fixes are correctly merged in nodes.go

dd/d4fa4a7bbb/metadata.json

@@ -0,0 +1,26 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "ddd4fa4a7bbb",
+  "strategy": "manual-commit",
+  "branch": "hotfix",
+  "checkpoints_count": 2,
+  "files_touched": [
+    "internal/repository/node.go"
+  ],
+  "sessions": [
+    {
+      "metadata": "/dd/d4fa4a7bbb/0/metadata.json",
+      "transcript": "/dd/d4fa4a7bbb/0/full.jsonl",
+      "context": "/dd/d4fa4a7bbb/0/context.md",
+      "content_hash": "/dd/d4fa4a7bbb/0/content_hash.txt",
+      "prompt": "/dd/d4fa4a7bbb/0/prompt.txt"
+    }
+  ],
+  "token_usage": {
+    "input_tokens": 20,
+    "cache_creation_tokens": 117849,
+    "cache_read_tokens": 888905,
+    "output_tokens": 4998,
+    "api_call_count": 16
+  }
+}

e3/68e6d8abf3/0/content_hash.txt

@@ -0,0 +1 @@
+sha256:c4cc521b26e386a5f6fa3635a2ff2afbe9b783bab0426469aadcbd1386f5ec9a

e3/68e6d8abf3/0/context.md

@@ -0,0 +1,14 @@
+# Session Context
+
+## User Prompts
+
+### Prompt 1
+
+Implement the following plan:
+
+# Make SQLite Memory Limits Configurable via config.json
+
+## Context
+
+Fixes 1-4 for the SQLite memory leak are already implemented on this branch. The hardcoded defaults (200MB cache per connection, 1GB soft heap limit) are conservative. On the production server with 512GB RAM, these could be tuned higher for better query performance. Additionally, `RepositoryConfig` and `SetConfig()` exist but are **never wired up** — there's currently no way to override any re...
+

e3/68e6d8abf3/0/metadata.json

@@ -0,0 +1,37 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "e368e6d8abf3",
+  "session_id": "50b2b10a-1be0-441f-aafb-3c5828f0fcc9",
+  "strategy": "manual-commit",
+  "created_at": "2026-03-11T05:14:06.988885Z",
+  "branch": "optimize-db-indices",
+  "checkpoints_count": 1,
+  "files_touched": [
+    "cmd/cc-backend/main.go",
+    "internal/config/config.go",
+    "internal/config/schema.go",
+    "internal/repository/config.go",
+    "internal/repository/dbConnection.go",
+    "internal/repository/jobFind.go",
+    "internal/repository/jobQuery.go",
+    "internal/repository/stats.go"
+  ],
+  "agent": "Claude Code",
+  "turn_id": "2a56dd0625b9",
+  "token_usage": {
+    "input_tokens": 15,
+    "cache_creation_tokens": 27408,
+    "cache_read_tokens": 402383,
+    "output_tokens": 3673,
+    "api_call_count": 13
+  },
+  "initial_attribution": {
+    "calculated_at": "2026-03-11T05:14:06.919539Z",
+    "agent_lines": 94,
+    "human_added": 41,
+    "human_modified": 0,
+    "human_removed": 0,
+    "total_committed": 135,
+    "agent_percentage": 69.62962962962963
+  }
+}

e3/68e6d8abf3/0/prompt.txt

@@ -0,0 +1,188 @@
+Implement the following plan:
+
+# Make SQLite Memory Limits Configurable via config.json
+
+## Context
+
+Fixes 1-4 for the SQLite memory leak are already implemented on this branch. The hardcoded defaults (200MB cache per connection, 1GB soft heap limit) are conservative. On the production server with 512GB RAM, these could be tuned higher for better query performance. Additionally, `RepositoryConfig` and `SetConfig()` exist but are **never wired up** — there's currently no way to override any repository defaults from config.json.
+
+## Current State (already implemented on this branch)
+
+- `_cache_size = -200000` (200MB per connection, hardcoded) — **too low for 80GB DB, will be made configurable**
+- `soft_heap_limit = 1073741824` (1GB process-wide, hardcoded) — **too low, will be made configurable**
+- `ConnectionMaxIdleTime = 10 * time.Minute` (hardcoded default)
+- `MaxOpenConnections = 4` (hardcoded default)
+- Context propagation to all query call sites (already done)
+
+## Problem
+
+`repository.SetConfig()` exists but is never called from `main.go`. The `initDatabase()` function (line 110) just calls `repository.Connect(config.Keys.DB)` directly. There's no `"db-config"` section in `ProgramConfig` or the JSON schema.
+
+## Proposed Changes
+
+### 1. Add SQLite memory fields to `RepositoryConfig`
+
+**File:** `internal/repository/config.go`
+
+Add two new fields with sensible defaults:
+
+```go
+type RepositoryConfig struct {
+    // ... existing fields ...
+
+    // DbCacheSizeMB is the SQLite page cache size per connection in MB.
+    // Uses negative PRAGMA cache_size notation (KiB). With MaxOpenConnections=4
+    // and DbCacheSizeMB=200, total page cache is up to 800MB.
+    // Default: 200 (MB)
+    DbCacheSizeMB int
+
+    // DbSoftHeapLimitMB is the process-wide SQLite soft heap limit in MB.
+    // SQLite will try to release cache pages to stay under this limit.
+    // It's a soft limit — queries won't fail, but cache eviction becomes more aggressive.
+    // Default: 1024 (1GB)
+    DbSoftHeapLimitMB int
+}
+```
+
+Update `DefaultConfig()`:
+```go
+DbCacheSizeMB:     2048,  // 2GB per connection
+DbSoftHeapLimitMB: 16384, // 16GB process-wide
+```
+
+**Rationale for defaults:** With an 80GB production database on a 512GB server, we want the cache to hold a significant portion of the DB. At 4 connections × 2GB = 8GB default page cache, plus 16GB soft heap limit. The previous 200MB/1GB hardcoded values were too conservative and would hurt query performance by forcing excessive cache eviction. These defaults use ~5% of a 512GB server — still safe for smaller machines, while enabling good performance on production.
+
+### 2. Use config values in `Connect()` and `setupSqlite()`
+
+**File:** `internal/repository/dbConnection.go`
+
+In `Connect()`, replace the hardcoded cache_size:
+```go
+cacheSizeKiB := repoConfig.DbCacheSizeMB * 1024  // Convert MB to KiB
+connectionURLParams.Add("_cache_size", fmt.Sprintf("-%d", cacheSizeKiB))
+```
+
+Change `setupSqlite()` to accept the config and use it for soft_heap_limit:
+```go
+func setupSqlite(db *sql.DB, cfg *RepositoryConfig) error {
+    pragmas := []string{
+        "temp_store = memory",
+        fmt.Sprintf("soft_heap_limit = %d", cfg.DbSoftHeapLimitMB*1024*1024),
+    }
+    // ...
+}
+```
+
+Update the call site in `Connect()`:
+```go
+err = setupSqlite(dbHandle.DB, &opts)  // was: setupSqlite(dbHandle.DB)
+```
+
+### 3. Add `"db-config"` section to `ProgramConfig` and JSON schema
+
+**File:** `internal/config/config.go`
+
+Add a new struct and field to `ProgramConfig`:
+
+```go
+type DbConfig struct {
+    CacheSizeMB       int `json:"cache-size-mb"`
+    SoftHeapLimitMB   int `json:"soft-heap-limit-mb"`
+    MaxOpenConnections int `json:"max-open-connections"`
+    MaxIdleConnections int `json:"max-idle-connections"`
+    ConnectionMaxIdleTimeMins int `json:"max-idle-time-minutes"`
+}
+
+type ProgramConfig struct {
+    // ... existing fields ...
+    DbConfig *DbConfig `json:"db-config"`
+}
+```
+
+**File:** `internal/config/schema.go`
+
+Add the schema section for validation.
+
+### 4. Wire `SetConfig()` in `initDatabase()`
+
+**File:** `cmd/cc-backend/main.go`
+
+```go
+func initDatabase() error {
+    if config.Keys.DbConfig != nil {
+        cfg := repository.DefaultConfig()
+        dc := config.Keys.DbConfig
+        if dc.CacheSizeMB > 0 {
+            cfg.DbCacheSizeMB = dc.CacheSizeMB
+        }
+        if dc.SoftHeapLimitMB > 0 {
+            cfg.DbSoftHeapLimitMB = dc.SoftHeapLimitMB
+        }
+        if dc.MaxOpenConnections > 0 {
+            cfg.MaxOpenConnections = dc.MaxOpenConnections
+        }
+        if dc.MaxIdleConnections > 0 {
+            cfg.MaxIdleConnections = dc.MaxIdleConnections
+        }
+        if dc.ConnectionMaxIdleTimeMins > 0 {
+            cfg.ConnectionMaxIdleTime = time.Duration(dc.ConnectionMaxIdleTimeMins) * time.Minute
+        }
+        repository.SetConfig(cfg)
+    }
+    repository.Connect(config.Keys.DB)
+    return nil
+}
+```
+
+### 5. Log effective values on startup
+
+**File:** `internal/repository/dbConnection.go`
+
+After setting PRAGMAs, log the effective values so operators can verify:
+```go
+cclog.Infof("SQLite config: cache_size=%dMB/conn, soft_heap_limit=%dMB, max_conns=%d",
+    repoConfig.DbCacheSizeMB, repoConfig.DbSoftHeapLimitMB, repoConfig.MaxOpenConnections)
+```
+
+## Example config.json (for 512GB server with 80GB database)
+
+```json
+{
+  "main": {
+    "db": "./var/job.db",
+    "db-config": {
+      "cache-size-mb": 16384,
+      "soft-heap-limit-mb": 131072,
+      "max-open-connections": 8,
+      "max-idle-time-minutes": 30
+    }
+  }
+}
+```
+
+This would give: 8 connections × 16GB cache = 128GB max page cache, with a 128GB soft heap limit. The entire 80GB database can be cached in memory. On a 512GB server that's ~25% of RAM.
+
+**Sizing guidance (for documentation):**
+- `cache-size-mb`: Set to `DB_size / max-open-connections` to allow the entire DB to be cached. E.g., 80GB DB with 8 connections → 10GB per connection minimum.
+- `soft-heap-limit-mb`: Set to total desired SQLite memory budget. Should be ≥ `cache-size-mb × max-open-connections` to avoid cache thrashing.
+
+## Files to Modify
+
+| File | Changes |
+|------|---------|
+| `internal/repository/config.go` | Add `DbCacheSizeMB`, `DbSoftHeapLimitMB` fields + defaults |
+| `internal/repository/dbConnection.go` | Use config values instead of hardcoded; pass config to `setupSqlite`; add startup log |
+| `internal/config/config.go` | Add `DbConfig` struct and field to `ProgramConfig` |
+| `internal/config/schema.go` | Add `"db-config"` JSON schema section |
+| `cmd/cc-backend/main.go` | Wire `SetConfig()` in `initDatabase()` |
+
+## Verification
+
+1. `go build ./...` — compiles
+2. `go test ./internal/repository/... ./internal/config/...` — tests pass
+3. Without `db-config` in config.json: defaults apply (200MB cache, 1GB heap) — backwards compatible
+4. With `db-config`: verify with `PRAGMA cache_size;` and `PRAGMA soft_heap_limit;` in sqlite3 CLI
+5. Check startup log shows effective values
+
+
+If you need specific details from before exiting plan mode (like exact code snippets, error messages, or content you generated), read the full transcript at: /Users/jan/.claude/projects/-Users-jan-prg-CC-cc-backend/520afa6a-6a70-437b-96c1-35c40ed3ec48.jsonl

e3/68e6d8abf3/1/content_hash.txt

@@ -0,0 +1 @@
+sha256:f187013ac2acf6db7e6f13db2bfe1ab2c10050fe3d8ffd3d41122449dcf54b3c

e3/68e6d8abf3/1/context.md

@@ -0,0 +1,24 @@
+# Session Context
+
+## User Prompts
+
+### Prompt 1
+
+Implement the following plan:
+
+# Fix SQLite Memory Not Released After Query Timeout
+
+## Context
+
+On the production 20M-row database, when a query runs into a timeout (due to full-table scan with wrong index), the memory allocated by SQLite is **not released afterwards**. The process stays bloated until restarted. This is caused by three compounding issues in the current SQLite configuration.
+
+## Root Cause Analysis
+
+### 1. `_cache_size=1000000000` is effectively unlimited (~4TB)
+
+**File:** `i...
+
+### Prompt 2
+
+Our server has 512GB main memory. Does it make sense to make cache_size and soft_heap_limit configurable to make use of the main memory capacity?
+

e3/68e6d8abf3/1/metadata.json

@@ -0,0 +1,34 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "e368e6d8abf3",
+  "session_id": "520afa6a-6a70-437b-96c1-35c40ed3ec48",
+  "strategy": "manual-commit",
+  "created_at": "2026-03-11T05:14:07.476561Z",
+  "branch": "optimize-db-indices",
+  "checkpoints_count": 2,
+  "files_touched": [
+    "internal/repository/config.go",
+    "internal/repository/dbConnection.go",
+    "internal/repository/jobFind.go",
+    "internal/repository/jobQuery.go",
+    "internal/repository/stats.go"
+  ],
+  "agent": "Claude Code",
+  "turn_id": "443ef781634b",
+  "token_usage": {
+    "input_tokens": 5108,
+    "cache_creation_tokens": 68335,
+    "cache_read_tokens": 1908216,
+    "output_tokens": 13846,
+    "api_call_count": 34
+  },
+  "initial_attribution": {
+    "calculated_at": "2026-03-11T05:14:07.210716Z",
+    "agent_lines": 37,
+    "human_added": 98,
+    "human_modified": 0,
+    "human_removed": 0,
+    "total_committed": 135,
+    "agent_percentage": 27.40740740740741
+  }
+}

e3/68e6d8abf3/1/prompt.txt

@@ -0,0 +1,136 @@
+Implement the following plan:
+
+# Fix SQLite Memory Not Released After Query Timeout
+
+## Context
+
+On the production 20M-row database, when a query runs into a timeout (due to full-table scan with wrong index), the memory allocated by SQLite is **not released afterwards**. The process stays bloated until restarted. This is caused by three compounding issues in the current SQLite configuration.
+
+## Root Cause Analysis
+
+### 1. `_cache_size=1000000000` is effectively unlimited (~4TB)
+
+**File:** `internal/repository/dbConnection.go:82`
+
+```go
+connectionURLParams.Add("_cache_size", "1000000000")
+```
+
+SQLite's `cache_size` PRAGMA interprets **positive values as page count** (default page size = 4KB). So 1,000,000,000 pages × 4KB = ~4TB. In practice, this means "never evict cached pages." After a full-table scan of 20M rows, every page touched stays in SQLite's page cache. With 4 connections (`MaxOpenConns=4`), each can independently cache gigabytes.
+
+For comparison, the SQLite archive backend in `pkg/archive/sqliteBackend.go` uses `PRAGMA cache_size=-64000` (64MB — negative = KiB).
+
+### 2. No query context/timeout — queries run indefinitely
+
+**File:** `internal/repository/jobQuery.go:87`
+
+```go
+rows, err := query.RunWith(r.stmtCache).Query()  // No context!
+```
+
+The `ctx` parameter is available but never passed to the database layer. Squirrel supports `.QueryContext(ctx)` but it's not used. If the HTTP request times out or the client disconnects, the query keeps running and scanning pages into cache.
+
+### 3. No SQLite memory limit — no `soft_heap_limit` or `shrink_memory`
+
+SQLite has built-in memory management PRAGMAs that are not configured:
+- **`soft_heap_limit`** — asks SQLite to keep heap usage below N bytes (best-effort, releases cache pages to stay under limit)
+- **`hard_heap_limit`** — hard cap, queries fail with SQLITE_NOMEM if exceeded
+- **`shrink_memory`** — immediately releases all unused memory back to the OS
+
+None of these are set, so SQLite allocates freely and never releases.
+
+### 4. `temp_store = memory` amplifies the problem
+
+**File:** `internal/repository/dbConnection.go:41`
+
+Temporary B-tree sorts (exactly what happens during ORDER BY on a full-table scan) are stored in RAM. With 20M rows and no sort optimization, this can be gigabytes of temporary memory on top of the page cache.
+
+### 5. Connections live for 1 hour after use
+
+`ConnMaxIdleTime = 1 hour` means a connection that just did a massive full-table scan sits idle in the pool for up to an hour, holding all its cached pages.
+
+## Proposed Changes
+
+### Fix 1: Set reasonable `cache_size` (high impact, low risk)
+
+**File:** `internal/repository/dbConnection.go:82`
+
+Change from `1000000000` (1B pages ≈ 4TB) to `-200000` (200MB in KiB notation, per connection):
+
+```go
+connectionURLParams.Add("_cache_size", "-200000")  // 200MB per connection
+```
+
+With 4 max connections: 4 × 200MB = 800MB max page cache. This is generous enough for normal queries but prevents runaway memory after full-table scans.
+
+### Fix 2: Add `soft_heap_limit` (high impact, low risk)
+
+**File:** `internal/repository/dbConnection.go`, in `setupSqlite()`:
+
+```go
+"soft_heap_limit = 1073741824",  // 1GB soft limit across all connections
+```
+
+This is a **process-wide** limit (not per-connection). SQLite will try to release cache pages to stay under 1GB total. It's a soft limit — it won't abort queries, just evicts cache more aggressively.
+
+### Fix 3: Pass context to database queries (medium impact, medium effort)
+
+Change `.Query()` to `.QueryContext(ctx)`, `.QueryRow()` to `.QueryRowContext(ctx)`, and `.Scan()` to `.ScanContext(ctx)` for all query methods that already receive a `ctx` parameter. This allows HTTP request cancellation to stop the SQLite query.
+
+**Note:** The `stmtCache` from squirrel supports `QueryContext`/`QueryRowContext`. Only methods that already have `ctx` are changed — no signature changes needed.
+
+**Call sites to update** (methods that have `ctx` and call `.Query()`/`.QueryRow()`/`.Scan()`):
+
+| File | Method | Line | Change |
+|------|--------|------|--------|
+| `jobQuery.go` | `QueryJobs` | 87 | `.Query()` → `.QueryContext(ctx)` |
+| `jobQuery.go` | `CountJobs` | 129 | `.Scan()` → `.ScanContext(ctx)` |
+| `stats.go` | `JobsStatsGrouped` | 233 | `.Query()` → `.QueryContext(ctx)` |
+| `stats.go` | `JobsStats` | 358 | `.QueryRow()` → `.QueryRowContext(ctx)` |
+| `stats.go` | `JobCountGrouped` | 443 | `.Query()` → `.QueryContext(ctx)` |
+| `stats.go` | `AddJobCountGrouped` | 504 | `.Query()` → `.QueryContext(ctx)` |
+| `stats.go` | `AddJobCount` | 569 | `.Scan()` → `.ScanContext(ctx)` |
+| `stats.go` | `jobsStatisticsHistogram` | 758 | `.Query()` → `.QueryContext(ctx)` |
+| `stats.go` | `jobsDurationStatisticsHistogram` | 832 | `.Query()` → `.QueryContext(ctx)` |
+| `stats.go` | `jobsMetricStatisticsHistogram` | 962 | `.Query()` → `.QueryContext(ctx)` |
+| `jobFind.go` | `FindByID` | 174 | `.QueryRow()` → `.QueryRowContext(ctx)` |
+| `jobFind.go` | `FindByJobID` | 220 | `.QueryRow()` → `.QueryRowContext(ctx)` |
+| `job.go` | `CountGroupedJobs` | 410 | `.Scan()` → `.ScanContext(ctx)` (needs ctx added to signature) |
+| `job.go` | `GetJobList` | 751 | `.Query()` → `.QueryContext(ctx)` (needs ctx added to signature) |
+
+Methods without `ctx` in their signature (e.g., `GetJobList`, `CountGroupedJobs`) can either have `ctx` added or be left for a follow-up. The priority is the methods already accepting `ctx`.
+
+### Fix 4: Reduce `ConnMaxIdleTime`
+
+**File:** `internal/repository/config.go`
+
+Reduce `ConnectionMaxIdleTime` from 1 hour to 10 minutes. Idle connections with cached pages are released sooner.
+
+## Scope — All Four Fixes
+
+All fixes are complementary, independent, and low-risk. No disadvantages to applying all together.
+
+## Files to Modify
+
+- `internal/repository/dbConnection.go` — cache_size, soft_heap_limit (Fixes 1 & 2)
+- `internal/repository/jobQuery.go` — QueryContext (Fix 3)
+- `internal/repository/job.go` — QueryContext for other query methods (Fix 3)
+- `internal/repository/stats.go` — QueryContext for stats queries (Fix 3)
+- `internal/repository/config.go` — ConnMaxIdleTime (Fix 4, optional)
+
+## Verification
+
+1. `go build ./...` — compiles
+2. `go test ./internal/repository/...` — tests pass
+3. Monitor RSS memory before/after on production:
+   - Trigger a heavy query, observe memory spike
+   - Verify memory drops back down within seconds (not hours)
+4. `PRAGMA cache_size;` in sqlite3 CLI on running DB — should show `-200000`
+5. `PRAGMA soft_heap_limit;` — should show `1073741824`
+
+
+If you need specific details from before exiting plan mode (like exact code snippets, error messages, or content you generated), read the full transcript at: /Users/jan/.claude/projects/-Users-jan-prg-CC-cc-backend/c31c699a-f492-48f7-bcf0-35d3ceeac243.jsonl
+
+---
+
+Our server has 512GB main memory. Does it make sense to make cache_size and soft_heap_limit configurable to make use of the main memory capacity?

e3/68e6d8abf3/metadata.json

@@ -0,0 +1,40 @@
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+  "strategy": "manual-commit",
+  "branch": "optimize-db-indices",
+  "checkpoints_count": 3,
+  "files_touched": [
+    "cmd/cc-backend/main.go",
+    "internal/config/config.go",
+    "internal/config/schema.go",
+    "internal/repository/config.go",
+    "internal/repository/dbConnection.go",
+    "internal/repository/jobFind.go",
+    "internal/repository/jobQuery.go",
+    "internal/repository/stats.go"
+  ],
+  "sessions": [
+    {
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ea/70a955214d/0/content_hash.txt

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+sha256:6b13f37bb9b6568e0cd504fb4abdbbf649442cfc23222562a396f6dec7f1e395

ea/70a955214d/0/context.md

@@ -0,0 +1,22 @@
+# Session Context
+
+## User Prompts
+
+### Prompt 1
+
+Implement the following plan:
+
+# Fix Missing `rows.Close()` Memory Leaks in SQLite3 Queries
+
+## Context
+
+Production memory leaks traced to queries that do full table scans (e.g., job state list sorted by `start_time` on all jobs). The root cause is `sql.Rows` objects not being closed after query execution. In Go's `database/sql`, every `rows` returned by `.Query()` holds a database connection and associated buffers until `rows.Close()` is called. Without `defer rows.Close()`, these leak on ev...
+
+### Prompt 2
+
+Check if the fixes are correctly merged in nodes.go
+
+### Prompt 3
+
+There also have to be bugs in jobQuery.go . Especially the following query triggers the memory leak: SELECT * FROM job WHERE job.job_state IN ("completed", "running", "failed") ORDER BY job.start_time DESC LIMIT 1 OFFSET 10; Dig deeper to find the cause. Also investigate why no existing index is used for this query.
+

ea/70a955214d/0/metadata.json

@@ -0,0 +1,31 @@
+{
+  "cli_version": "0.4.8",
+  "checkpoint_id": "ea70a955214d",
+  "session_id": "42401d2e-7d1c-4c0e-abe6-356cb2d48747",
+  "strategy": "manual-commit",
+  "created_at": "2026-03-11T04:28:54.113637Z",
+  "branch": "hotfix",
+  "checkpoints_count": 2,
+  "files_touched": [
+    "internal/repository/dbConnection.go",
+    "internal/repository/user.go"
+  ],
+  "agent": "Claude Code",
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+    "human_modified": 0,
+    "human_removed": 0,
+    "total_committed": 265,
+    "agent_percentage": 3.3962264150943398
+  }
+}

ea/70a955214d/0/prompt.txt

@@ -0,0 +1,101 @@
+Implement the following plan:
+
+# Fix Missing `rows.Close()` Memory Leaks in SQLite3 Queries
+
+## Context
+
+Production memory leaks traced to queries that do full table scans (e.g., job state list sorted by `start_time` on all jobs). The root cause is `sql.Rows` objects not being closed after query execution. In Go's `database/sql`, every `rows` returned by `.Query()` holds a database connection and associated buffers until `rows.Close()` is called. Without `defer rows.Close()`, these leak on every code path (both success and error returns).
+
+## Findings
+
+**22 total `.Query()` calls** across the repository layer. **15 have `defer rows.Close()`**. **7 do not** (listed below). Additionally, 1 `Queryx` call in `tags.go` is also missing close.
+
+In `node.go`, `QueryNodes` and `QueryNodesWithMeta` have partial `rows.Close()` only in error paths but **not on the success path** and not via `defer`.
+
+`CountStates` and `CountStatesTimed` in `node.go` also lack `defer rows.Close()` (same partial pattern as above for CountStates, none at all for CountStatesTimed).
+
+## Changes Required
+
+### 1. `internal/repository/stats.go` — 6 functions missing `defer rows.Close()`
+
+Add `defer rows.Close()` immediately after the `if err != nil` check for each:
+
+| Line | Function |
+|------|----------|
+| 233 | `JobsStatsGrouped` |
+| 438 | `JobCountGrouped` |
+| 494 | `AddJobCountGrouped` |
+| 553 | `AddJobCount` |
+| 753 | `jobsStatisticsHistogram` |
+| 821 | `jobsDurationStatisticsHistogram` |
+| 946 | `jobsMetricStatisticsHistogram` |
+
+Pattern — after each `Query()` error check, add:
+```go
+rows, err := query.RunWith(r.DB).Query()
+if err != nil {
+    ...
+    return nil, err
+}
+defer rows.Close()   // <-- ADD THIS
+```
+
+### 2. `internal/repository/tags.go` — 2 leaks in `CountTags()`
+
+**Line 282**: `xrows` from `r.DB.Queryx(...)` — add `defer xrows.Close()` after error check.
+
+**Line 333**: `rows` from `q.RunWith(r.stmtCache).Query()` — add `defer rows.Close()` after error check.
+
+### 3. `internal/repository/tags.go` — 3 leaks in `GetTags`, `GetTagsDirect`, `getArchiveTags`
+
+**Line 508** (`GetTags`): add `defer rows.Close()` after error check.
+**Line 541** (`GetTagsDirect`): add `defer rows.Close()` after error check.
+**Line 579** (`getArchiveTags`): add `defer rows.Close()` after error check.
+
+### 4. `internal/repository/node.go` — 4 functions missing `defer rows.Close()`
+
+**Line 363** (`QueryNodes`): Replace the manual `rows.Close()` in the error path with `defer rows.Close()` immediately after the error check. Remove the explicit `rows.Close()` call on line 375.
+
+**Line 412** (`QueryNodesWithMeta`): Same pattern — add `defer rows.Close()` after error check, remove explicit `rows.Close()` on line 427.
+
+**Line 558** (`CountStates`): Add `defer rows.Close()` after error check. Remove explicit `rows.Close()` on line 569.
+
+**Line 620** (`CountStatesTimed`): Add `defer rows.Close()` after error check. Remove explicit `rows.Close()` on line 633.
+
+## Summary of All Edits
+
+| File | Function | Action |
+|------|----------|--------|
+| `stats.go:237` | `JobsStatsGrouped` | Add `defer rows.Close()` |
+| `stats.go:442` | `JobCountGrouped` | Add `defer rows.Close()` |
+| `stats.go:498` | `AddJobCountGrouped` | Add `defer rows.Close()` |
+| `stats.go:557` | `AddJobCount` | Add `defer rows.Close()` |
+| `stats.go:757` | `jobsStatisticsHistogram` | Add `defer rows.Close()` |
+| `stats.go:825` | `jobsDurationStatisticsHistogram` | Add `defer rows.Close()` |
+| `stats.go:950` | `jobsMetricStatisticsHistogram` | Add `defer rows.Close()` |
+| `tags.go:284` | `CountTags` (xrows) | Add `defer xrows.Close()` |
+| `tags.go:336` | `CountTags` (rows) | Add `defer rows.Close()` |
+| `tags.go:513` | `GetTags` | Add `defer rows.Close()` |
+| `tags.go:546` | `GetTagsDirect` | Add `defer rows.Close()` |
+| `tags.go:584` | `getArchiveTags` | Add `defer rows.Close()` |
+| `node.go:368` | `QueryNodes` | Add `defer rows.Close()`, remove manual close on L375 |
+| `node.go:417` | `QueryNodesWithMeta` | Add `defer rows.Close()`, remove manual close on L427 |
+| `node.go:563` | `CountStates` | Add `defer rows.Close()`, remove manual close on L569 |
+| `node.go:625` | `CountStatesTimed` | Add `defer rows.Close()`, remove manual close on L633 |
+
+## Verification
+
+1. `go build ./...` — ensure it compiles
+2. `go test ./internal/repository/...` — run repository tests
+3. `go vet ./internal/repository/...` — static analysis
+
+
+If you need specific details from before exiting plan mode (like exact code snippets, error messages, or content you generated), read the full transcript at: /Users/jan/.claude/projects/-Users-jan-prg-CC-cc-backend/28147033-ddc8-4056-b064-e0558fbc614e.jsonl
+
+---
+
+Check if the fixes are correctly merged in nodes.go
+
+---
+
+There also have to be bugs in jobQuery.go . Especially the following query triggers the memory leak: SELECT * FROM job WHERE job.job_state IN ("completed", "running", "failed") ORDER BY job.start_time DESC LIMIT 1 OFFSET 10; Dig deeper to find the cause. Also investigate why no existing index is used for this query.

ea/70a955214d/metadata.json

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+  "branch": "hotfix",
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+    "internal/repository/user.go"
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+}