@pingvinen/donna-assistant 0.9.1 → 0.11.0

package/workflows/begin-the-day.md

@@ -4,82 +4,25 @@
 Carry forward open tasks from the previous day, surface recurring tasks due today, deduplicate, and present a concise daily brief.
 </objective>
 
-<step name="read-config">
-Read `~/.config/donna/config.md`.
-
-If the file does not exist, print:
-```
-✗ Donna is not configured. Run /donna:setup first.
-```
-Stop.
-
-Extract the `storage_repo`, `daily_folder` (default: `daily`), and `auto_push` (default: false) fields from the YAML frontmatter.
-
-**Obsidian sync:** Check if `<storage_repo>/.obsidian/daily-notes.json` exists.
-- If it exists and has a `folder` field that differs from `<daily_folder>`: update `<daily_folder>` to match Obsidian's value, and update `~/.config/donna/config.md` with the new `daily_folder`. Print `✓ Synced daily folder with Obsidian: <daily_folder>`.
-- If `<storage_repo>/.obsidian/` exists but `daily-notes.json` does not exist or has no `folder` field: write `<storage_repo>/.obsidian/daily-notes.json` with `{"folder":"<daily_folder>"}`. Print `✓ Configured Obsidian daily notes to use <daily_folder>/`.
-- Otherwise: do nothing.
-</step>
-
-<step name="check-pending-migrations">
-Read `~/.donna/state.md` with the Read tool. If the file does not exist or has no `pending_migrations` field in its YAML frontmatter, skip this step.
-
-For each entry in `pending_migrations`:
-
-**`move-standing-files`:** Move standing files from storage repo root to donna/ subfolder.
-
+<step name="init">
 Run via Bash:
 ```bash
-STORAGE_REPO="<storage_repo>"
-DONNA_DIR="$STORAGE_REPO/donna"
-MOVED=0
-
-mkdir -p "$DONNA_DIR"
-for FILE in role.md recurring.md role-research.md; do
-    if [ -f "$STORAGE_REPO/$FILE" ] && [ ! -f "$DONNA_DIR/$FILE" ]; then
-        mv "$STORAGE_REPO/$FILE" "$DONNA_DIR/$FILE"
-        echo "Moved $FILE to donna/$FILE"
-        MOVED=$((MOVED + 1))
-    fi
-done
-
-echo "MOVED=$MOVED"
+INIT=$(node ~/.donna/donna-tools.cjs init)
 ```
 
-If MOVED > 0, commit the move:
-```bash
-git -C <storage_repo> add -A
-git -C <storage_repo> diff --cached --quiet || git -C <storage_repo> commit -m "donna(migrate): move standing files to donna/ subfolder"
+Parse the JSON response. If the `error` field is `"not_configured"`, print:
 ```
-
-If `auto_push` is true in config, also push.
-
-**`backfill-tool-type`:** Backfill `type` on existing tool sections in tools.md using heuristic detection.
-
-Read `<storage_repo>/donna/tools.md` with the Read tool. If the file does not exist or has no tool sections, skip this handler.
-
-For each tool section (starting with `## <tool_name>`), check if a `- type:` line already exists. If the `- type:` line is missing, detect the correct type:
-
-1. If the tool section contains a `- command:` line where the value starts with `mcp:` (e.g., `- command: mcp:linear`), insert `- type: mcp` immediately after the `- command:` line.
-2. Else, if the tool section contains a `- base_url:` line:
-   - If the capabilities section contains entries that look like GraphQL queries (contain `query {` or `mutation {`), insert `- type: graphql` immediately after `## <tool_name>` (REST/GraphQL tools have no `- command:` line).
-   - Otherwise, insert `- type: rest` immediately after `## <tool_name>`.
-3. Else (no `mcp:` prefix, no `base_url` field), insert `- type: cli` immediately after the `- command:` line.
-
-Write the updated file back with the Write tool. If any changes were made, commit:
-```bash
-git -C <storage_repo> add -A
-git -C <storage_repo> diff --cached --quiet || git -C <storage_repo> commit -m "donna(migrate): backfill tool types on existing tools"
+x Donna is not configured. Run /donna:setup first.
 ```
+Stop.
 
-If `auto_push` is true in config, also push.
+Extract `storage_repo`, `daily_folder`, `auto_push` from the JSON.
 
-After processing all pending migrations, update `~/.donna/state.md` with the Write tool: remove the completed entries from `pending_migrations`. If no entries remain, write:
-```markdown
----
-pending_migrations: []
----
+If `update_available` is non-null, print:
+```
+Donna v<update_available> available -- run npx @pingvinen/donna-assistant to update
 ```
+Continue normally.
 </step>
 
 <step name="get-today">
@@ -99,7 +42,11 @@ date +%-d
 ```
 Store the result as `<day_of_month>` (e.g., "1" for the 1st).
 
-Construct the daily file path: `<storage_repo>/<daily_folder>/<today>.md`.
+Get the daily file path via donna-tools:
+```bash
+DAILY_PATH=$(node ~/.donna/donna-tools.cjs daily-path | node -e "process.stdin.resume();let d='';process.stdin.on('data',c=>d+=c);process.stdin.on('end',()=>console.log(JSON.parse(d).path))")
+```
+Store the result as `<daily_file_path>`.
 </step>
 
 <step name="find-previous-file">
@@ -147,6 +94,26 @@ For each task, determine if it is due today using this logic:
 Store the descriptions of all due tasks as `<recurring_tasks>` (just the description text, without the interval suffix).
 </step>
 
+<step name="check-follow-ups">
+Read `<storage_repo>/donna/follow-ups.md` with the Read tool. If the file does not exist, set `<follow_up_tasks>` to an empty list, set `<follow_ups_modified>` to `false`, and continue (follow-ups are optional).
+
+Parse each line matching the pattern `- [ ] <description> | due: YYYY-MM-DD`. For each matching entry:
+
+- Parse the `due` date (YYYY-MM-DD).
+- If `due <= <today>`: add to `<follow_up_tasks>` as: `- [ ] <description>` (no annotation).
+- If `due > <today>`: task is future — leave the line in follow-ups.md. Do not add to `<follow_up_tasks>`.
+
+After collecting all due/past-due tasks, remove those matched lines from follow-ups.md (the matched lines are NOT written back — only future lines remain). Write the updated file back with the Write tool. If lines were removed, set `<follow_ups_modified>` to `true`. If no lines were removed, set `<follow_ups_modified>` to `false` and skip the file write. Per D-03: items are removed, not checked off or left with a marker.
+
+Store `<follow_up_tasks>` for use in the deduplicate step.
+
+CRITICAL constraints:
+- The step reads only one specific named file (`donna/follow-ups.md`) — no directory scan, no wildcard listing
+- File existence check is done via the Read tool (handle missing file gracefully)
+- macOS date command uses the exact same `date -j` pattern as the existing check-recurring step
+- Invalid date strings caught by `date -j`; skip the entry (do not surface, do not remove)
+</step>
+
 <step name="pull-tool-data">
 Read `<storage_repo>/donna/tools.md` with the Read tool.
 
@@ -178,9 +145,9 @@ Store the parsed tools and their capabilities as `<registered_tools>`.
 
 For `type: cli` capabilities (format: `<name>: <cli_invocation>`):
 
-Run via Bash with a 10-second timeout:
+Run via Bash (set the Bash tool's `timeout` parameter to `10000`):
 ```bash
-timeout 10 <cli_invocation> 2>&1
+<cli_invocation> 2>&1
 ```
 
 **On success (exit 0):**
@@ -210,9 +177,9 @@ Add the warning to `<tool_warnings>`. Continue to next capability/tool. Never re
 For `type: rest` capabilities (format: `<name>: <METHOD> /path`):
 1. Read `<storage_repo>/donna/secrets.md` with the Read tool. Parse key-value pairs from under the frontmatter.
 2. Resolve the `auth_secret` key to get the actual secret value. If the key is not found in secrets.md or the value is `REPLACE_WITH_YOUR_SECRET`, add warning `! <tool_name>: missing secret <auth_secret> — edit donna/secrets.md` and skip this tool.
-3. For each capability, run via Bash with a 10-second timeout:
+3. For each capability, run via Bash (set the Bash tool's `timeout` parameter to `10000`):
 ```bash
-timeout 10 curl -s -H "<auth_header>: <resolved_secret>" "<base_url><path>" 2>&1
+curl -s -H "<auth_header>: <resolved_secret>" "<base_url><path>" 2>&1
 ```
 4. Parse the JSON response using Claude's understanding to extract task-like items. Format:
 `- [ ] (<tool_name>) <description> [<identifier>](<url>)`
@@ -223,9 +190,9 @@ Continue. Never retry.
 
 For `type: graphql` capabilities (format: `<name>: <graphql_query>`):
 1. Same secrets resolution as REST.
-2. For each capability, run via Bash with a 10-second timeout:
+2. For each capability, run via Bash (set the Bash tool's `timeout` parameter to `10000`):
 ```bash
-timeout 10 curl -s -X POST -H "<auth_header>: <resolved_secret>" -H "Content-Type: application/json" -d '{"query":"<graphql_query>"}' "<base_url>" 2>&1
+curl -s -X POST -H "<auth_header>: <resolved_secret>" -H "Content-Type: application/json" -d '{"query":"<graphql_query>"}' "<base_url>" 2>&1
 ```
 3. Parse the JSON response to extract task-like items. Same format as REST.
 
@@ -265,7 +232,9 @@ Assemble the full task list using a single-pass deduplication to ensure idempote
 
 3. Add `<recurring_tasks>` as `- [ ] <description>` — for each recurring task, normalize its description and check whether any task already in the final list normalizes to the same value. If no match, add it. If a match exists, skip it.
 
-4. Add `<tool_tasks>` as-is — for each tool task, normalize its description and check whether any task already in the final list normalizes to the same value. If no match, add it. If a match exists, skip it.
+4. Add `<follow_up_tasks>` as-is — for each follow-up task, normalize its description and check whether any task already in the final list normalizes to the same value. If no match, add it. If a match exists, skip it.
+
+5. Add `<tool_tasks>` as-is — for each tool task, normalize its description and check whether any task already in the final list normalizes to the same value. If no match, add it. If a match exists, skip it.
 
 CRITICAL: A closed task `- [x] Review PRs` must block a recurring `- [ ] Review PRs` from being re-added. Both open AND closed existing tasks count for deduplication.
 
@@ -292,6 +261,7 @@ date: <today>
 <existing tasks, preserving their original order and open/closed state>
 <carried-forward tasks not already in existing>
 <recurring tasks not already in existing>
+<follow-up tasks not already in existing>
 
 ## From Tools
 <tool tasks not already in existing — only if there are tool tasks>
@@ -303,7 +273,7 @@ date: <today>
 <tool warnings — only if there are warnings>
 ```
 
-Tasks are written in this order: existing tasks first (preserving their original order and state), then carried-forward tasks, then recurring tasks.
+Tasks are written in this order: existing tasks first (preserving their original order and state), then carried-forward tasks, then recurring tasks, then follow-up tasks.
 
 If `<tool_tasks>` is empty and there are no resolved items, omit the `## From Tools` and `## Resolved` sections entirely.
 If `<tool_warnings>` is empty, omit the `## Warnings` section entirely. Each warning is written as-is (e.g., `! jira: command not found — install jira first`).
@@ -318,27 +288,17 @@ If no "every other" recurring tasks were added, skip this step.
 </step>
 
 <step name="git-commit">
-Run via Bash:
-```bash
-git -C <storage_repo> add -A
-```
-
-Check whether there is anything to commit:
+If `<follow_ups_modified>` is `true` (the check-follow-ups step modified follow-ups.md), run via Bash:
 ```bash
-git -C <storage_repo> status --porcelain
+node ~/.donna/donna-tools.cjs commit "donna(daily): <today> daily brief" --files <daily_folder>/<today>.md donna/follow-ups.md
 ```
 
-If the output is empty, skip the commit and continue.
-
-Otherwise, run:
+Otherwise (follow-ups.md was not modified), run via Bash:
 ```bash
-git -C <storage_repo> commit -m "donna(begin-the-day): daily brief for <today>"
+node ~/.donna/donna-tools.cjs commit "donna(daily): <today> daily brief" --files <daily_folder>/<today>.md
 ```
 
-If `auto_push` is true in config, also run:
-```bash
-git -C <storage_repo> push
-```
+Per D-07: follow-ups.md is included in the commit when items were surfaced and removed from the standing file.
 </step>
 
 <step name="print-brief">
@@ -363,6 +323,13 @@ If there are recurring tasks due today (tasks from `<recurring_tasks>` that were
 - [ ] Review sprint backlog
 ```
 
+If there are follow-up tasks (tasks from `<follow_up_tasks>` that were added to the final list), print:
+```
+## Follow-ups
+- [ ] Review design doc
+- [ ] Submit expense report
+```
+
 If there are tool tasks (tasks from `<tool_tasks>` that were added to the final list), print:
 ```
 ## From Tools
@@ -381,7 +348,7 @@ Always end with:
 ══════════════════════════════════════
 ```
 
-Show ALL tasks — never truncate. If no carried-forward tasks, omit the "## Carried Forward" section. If no recurring tasks due today, omit the "## Due Today" section. If no tool tasks, omit the "## From Tools" section. If no tool warnings, omit the "## Warnings" section. If carried-forward, recurring, AND tool tasks are all empty and there are no existing tasks, print:
+Show ALL tasks — never truncate. If no carried-forward tasks, omit the "## Carried Forward" section. If no recurring tasks due today, omit the "## Due Today" section. If no follow-up tasks, omit the "## Follow-ups" section. If no tool tasks, omit the "## From Tools" section. If no tool warnings, omit the "## Warnings" section. If carried-forward, recurring, follow-up, AND tool tasks are all empty and there are no existing tasks, print:
 ```
 No tasks for today — enjoy your day!
 ```

package/workflows/done.md

@@ -4,71 +4,33 @@
 Mark one or more tasks as complete in today's daily journal file and commit the change to git.
 </objective>
 
-<step name="read-config">
-Read `~/.config/donna/config.md`.
-
-If the file does not exist, print:
-```
-✗ Donna is not configured. Run /donna:setup first.
-```
-Stop.
-
-Extract the `storage_repo`, `daily_folder` (default: `daily`), and `auto_push` (default: false) fields from the YAML frontmatter.
-
-**Obsidian sync:** Check if `<storage_repo>/.obsidian/daily-notes.json` exists.
-- If it exists and has a `folder` field that differs from `<daily_folder>`: update `<daily_folder>` to match Obsidian's value, and update `~/.config/donna/config.md` with the new `daily_folder`. Print `✓ Synced daily folder with Obsidian: <daily_folder>`.
-- If `<storage_repo>/.obsidian/` exists but `daily-notes.json` does not exist or has no `folder` field: write `<storage_repo>/.obsidian/daily-notes.json` with `{"folder":"<daily_folder>"}`. Print `✓ Configured Obsidian daily notes to use <daily_folder>/`.
-- Otherwise: do nothing.
-</step>
-
-<step name="check-pending-migrations">
-Read `~/.donna/state.md` with the Read tool. If the file does not exist or has no `pending_migrations` field in its YAML frontmatter, skip this step.
-
-For each entry in `pending_migrations`:
-
-**`move-standing-files`:** Move standing files from storage repo root to donna/ subfolder.
-
+<step name="init">
 Run via Bash:
 ```bash
-STORAGE_REPO="<storage_repo>"
-DONNA_DIR="$STORAGE_REPO/donna"
-MOVED=0
-
-mkdir -p "$DONNA_DIR"
-for FILE in role.md recurring.md role-research.md; do
-    if [ -f "$STORAGE_REPO/$FILE" ] && [ ! -f "$DONNA_DIR/$FILE" ]; then
-        mv "$STORAGE_REPO/$FILE" "$DONNA_DIR/$FILE"
-        echo "Moved $FILE to donna/$FILE"
-        MOVED=$((MOVED + 1))
-    fi
-done
-
-echo "MOVED=$MOVED"
+INIT=$(node ~/.donna/donna-tools.cjs init)
 ```
 
-If MOVED > 0, commit the move:
-```bash
-git -C <storage_repo> add -A
-git -C <storage_repo> diff --cached --quiet || git -C <storage_repo> commit -m "donna(migrate): move standing files to donna/ subfolder"
+Parse the JSON response. If the `error` field is `"not_configured"`, print:
+```
+x Donna is not configured. Run /donna:setup first.
 ```
+Stop.
 
-If `auto_push` is true in config, also push.
+Extract `storage_repo`, `daily_folder`, `auto_push` from the JSON.
 
-After processing all pending migrations, update `~/.donna/state.md` with the Write tool: remove the completed entries from `pending_migrations`. If no entries remain, write:
-```markdown
----
-pending_migrations: []
----
+If `update_available` is non-null, print:
+```
+Donna v<update_available> available -- run npx @pingvinen/donna-assistant to update
 ```
+Continue normally.
 </step>
 
 <step name="find-daily-file">
-Run via Bash to get today's date:
+Get the daily file path via donna-tools:
 ```bash
-date +%Y-%m-%d
+DAILY_PATH=$(node ~/.donna/donna-tools.cjs daily-path | node -e "process.stdin.resume();let d='';process.stdin.on('data',c=>d+=c);process.stdin.on('end',()=>console.log(JSON.parse(d).path))")
 ```
-
-Store the result as `<date>`. Construct the daily file path: `<storage_repo>/<daily_folder>/<date>.md`.
+Store the result as `<daily_file_path>`. Extract `<date>` from the filename (last path component without `.md`).
 
 If the file does not exist, print:
 ```
@@ -135,30 +97,10 @@ Write the updated file with the Write tool.
 <step name="git-commit">
 Run via Bash:
 ```bash
-git -C <storage_repo> add -A
-```
-
-Check whether there is anything to commit:
-```bash
-git -C <storage_repo> status --porcelain
+node ~/.donna/donna-tools.cjs commit "donna(done): <task_summary>" --files <daily_folder>/<date>.md
 ```
 
-If the output is empty, skip the commit and continue.
-
-If one task was completed, run:
-```bash
-git -C <storage_repo> commit -m "donna(done): <description>"
-```
-
-If multiple tasks were completed, run:
-```bash
-git -C <storage_repo> commit -m "donna(done): <N> tasks completed"
-```
-
-If `auto_push` is true in config, also run:
-```bash
-git -C <storage_repo> push
-```
+Where `<task_summary>` is the completed task description (if one task) or `<N> tasks completed` (if multiple tasks).
 </step>
 
 <step name="confirm">

package/workflows/focus.md

@@ -4,92 +4,33 @@
 Read today's daily file, score open tasks on urgency and context signals, optionally re-query active tools for enriched data, and produce a short prioritized focus list written to daily/focus.md and printed to the terminal. This is a read-only operation relative to the daily file: only focus.md is written.
 </objective>
 
-<step name="read-config">
-Read `~/.config/donna/config.md`.
-
-If the file does not exist, print:
-```
-✗ Donna is not configured. Run /donna:setup first.
-```
-Stop.
-
-Extract the `storage_repo`, `daily_folder` (default: `daily`), and `auto_push` (default: false) fields from the YAML frontmatter.
-
-**Obsidian sync:** Check if `<storage_repo>/.obsidian/daily-notes.json` exists.
-- If it exists and has a `folder` field that differs from `<daily_folder>`: update `<daily_folder>` to match Obsidian's value, and update `~/.config/donna/config.md` with the new `daily_folder`. Print `✓ Synced daily folder with Obsidian: <daily_folder>`.
-- If `<storage_repo>/.obsidian/` exists but `daily-notes.json` does not exist or has no `folder` field: write `<storage_repo>/.obsidian/daily-notes.json` with `{"folder":"<daily_folder>"}`. Print `✓ Configured Obsidian daily notes to use <daily_folder>/`.
-- Otherwise: do nothing.
-</step>
-
-<step name="check-pending-migrations">
-Read `~/.donna/state.md` with the Read tool. If the file does not exist or has no `pending_migrations` field in its YAML frontmatter, skip this step.
-
-For each entry in `pending_migrations`:
-
-**`move-standing-files`:** Move standing files from storage repo root to donna/ subfolder.
-
+<step name="init">
 Run via Bash:
 ```bash
-STORAGE_REPO="<storage_repo>"
-DONNA_DIR="$STORAGE_REPO/donna"
-MOVED=0
-
-mkdir -p "$DONNA_DIR"
-for FILE in role.md recurring.md role-research.md; do
-    if [ -f "$STORAGE_REPO/$FILE" ] && [ ! -f "$DONNA_DIR/$FILE" ]; then
-        mv "$STORAGE_REPO/$FILE" "$DONNA_DIR/$FILE"
-        echo "Moved $FILE to donna/$FILE"
-        MOVED=$((MOVED + 1))
-    fi
-done
-
-echo "MOVED=$MOVED"
+INIT=$(node ~/.donna/donna-tools.cjs init)
 ```
 
-If MOVED > 0, commit the move:
-```bash
-git -C <storage_repo> add -A
-git -C <storage_repo> diff --cached --quiet || git -C <storage_repo> commit -m "donna(migrate): move standing files to donna/ subfolder"
+Parse the JSON response. If the `error` field is `"not_configured"`, print:
 ```
-
-If `auto_push` is true in config, also push.
-
-**`backfill-tool-type`:** Backfill `type` on existing tool sections in tools.md using heuristic detection.
-
-Read `<storage_repo>/donna/tools.md` with the Read tool. If the file does not exist or has no tool sections, skip this handler.
-
-For each tool section (starting with `## <tool_name>`), check if a `- type:` line already exists. If the `- type:` line is missing, detect the correct type:
-
-1. If the tool section contains a `- command:` line where the value starts with `mcp:` (e.g., `- command: mcp:linear`), insert `- type: mcp` immediately after the `- command:` line.
-2. Else, if the tool section contains a `- base_url:` line:
-   - If the capabilities section contains entries that look like GraphQL queries (contain `query {` or `mutation {`), insert `- type: graphql` immediately after `## <tool_name>` (REST/GraphQL tools have no `- command:` line).
-   - Otherwise, insert `- type: rest` immediately after `## <tool_name>`.
-3. Else (no `mcp:` prefix, no `base_url` field), insert `- type: cli` immediately after the `- command:` line.
-
-Write the updated file back with the Write tool. If any changes were made, commit:
-```bash
-git -C <storage_repo> add -A
-git -C <storage_repo> diff --cached --quiet || git -C <storage_repo> commit -m "donna(migrate): backfill tool types on existing tools"
+x Donna is not configured. Run /donna:setup first.
 ```
+Stop.
 
-If `auto_push` is true in config, also push.
+Extract `storage_repo`, `daily_folder`, `auto_push` from the JSON.
 
-After processing all pending migrations, update `~/.donna/state.md` with the Write tool: remove the completed entries from `pending_migrations`. If no entries remain, write:
-```markdown
----
-pending_migrations: []
----
+If `update_available` is non-null, print:
 ```
+Donna v<update_available> available -- run npx @pingvinen/donna-assistant to update
+```
+Continue normally.
 </step>
 
 <step name="read-daily-file">
-Get today's date via Bash:
+Get the daily file path via donna-tools:
 ```bash
-date +%Y-%m-%d
+DAILY_PATH=$(node ~/.donna/donna-tools.cjs daily-path | node -e "process.stdin.resume();let d='';process.stdin.on('data',c=>d+=c);process.stdin.on('end',()=>console.log(JSON.parse(d).path))")
 ```
-Store as `<today>`.
-
-Construct the daily file path: `<storage_repo>/<daily_folder>/<today>.md`.
+Store the result as `<daily_file_path>`. Extract `<today>` from the filename (last path component without `.md`).
 
 Read the daily file with the Read tool. If the file does not exist, print:
 ```
@@ -154,23 +95,25 @@ For each matched tool, extract:
 **Type-aware execution within each agent (or direct execution for single tool):**
 
 For `type: cli` capabilities (format: `<name>: <cli_invocation>`):
+
+Run via Bash (set the Bash tool's `timeout` parameter to `10000`):
 ```bash
-timeout 10 <cli_invocation> 2>&1
+<cli_invocation> 2>&1
 ```
 
 For `type: rest` capabilities (format: `<name>: <METHOD> /path`):
 1. Read `<storage_repo>/donna/secrets.md` with the Read tool. Parse key-value pairs from under the frontmatter.
 2. Resolve the `auth_secret` key to get the actual secret value. If the key is not found in secrets.md or the value is `REPLACE_WITH_YOUR_SECRET`, add warning `! <tool_name>: missing secret <auth_secret> — edit donna/secrets.md` and skip this tool.
-3. For each capability, run via Bash with a 10-second timeout:
+3. For each capability, run via Bash (set the Bash tool's `timeout` parameter to `10000`):
 ```bash
-timeout 10 curl -s -H "<auth_header>: <resolved_secret>" "<base_url><path>" 2>&1
+curl -s -H "<auth_header>: <resolved_secret>" "<base_url><path>" 2>&1
 ```
 
 For `type: graphql` capabilities (format: `<name>: <graphql_query>`):
 1. Same secrets resolution as REST.
-2. For each capability, run via Bash with a 10-second timeout:
+2. For each capability, run via Bash (set the Bash tool's `timeout` parameter to `10000`):
 ```bash
-timeout 10 curl -s -X POST -H "<auth_header>: <resolved_secret>" -H "Content-Type: application/json" -d '{"query":"<graphql_query>"}' "<base_url>" 2>&1
+curl -s -X POST -H "<auth_header>: <resolved_secret>" -H "Content-Type: application/json" -d '{"query":"<graphql_query>"}' "<base_url>" 2>&1
 ```
 
 For `type: mcp` capabilities (format: `<name>: mcp:<server>/<tool>`):
@@ -262,24 +205,7 @@ If there are tool warnings from `<tool_warnings>`, append them after the footer:
 <step name="git-commit">
 Run via Bash:
 ```bash
-git -C <storage_repo> add -A
-```
-
-Check whether there is anything to commit:
-```bash
-git -C <storage_repo> status --porcelain
-```
-
-If the output is empty, skip the commit and continue.
-
-Otherwise, run:
-```bash
-git -C <storage_repo> commit -m "donna(focus): focus list for <today>"
-```
-
-If `auto_push` is true in config, also run:
-```bash
-git -C <storage_repo> push
+node ~/.donna/donna-tools.cjs commit "donna(focus): updated focus list" --files <daily_folder>/<today>.md
 ```
 </step>