Search prompts for directory references

.claude/skills/deepwork_jobs.define/SKILL.md

@@ -150,6 +150,8 @@ For each major phase they mentioned, ask structured questions to gather details:
    - Where should each output be saved? (filename/path)
    - Should outputs be organized in subdirectories? (e.g., `reports/`, `data/`, `drafts/`)
    - Will other steps need this output?
+
+   **Important**: Output paths should always be within the main repository directory structure, not in dot-directories like `.deepwork/`. Dot-directories are for configuration and job definitions, not for job outputs. Use paths like `research/competitors/report.md` rather than `.deepwork/outputs/report.md`.
    - **Does this output have a doc spec?** If a doc spec was created in Step 1.6/1.7, reference it for the appropriate output
 
 4. **Step Dependencies**
@@ -488,7 +490,7 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
   6. **Complete Steps**: Each step must have: id (lowercase_underscores), name, description, instructions_file, outputs (at least one), and dependencies array
   7. **Valid Dependencies**: Dependencies must reference existing step IDs with no circular references
   8. **Input Consistency**: File inputs with `from_step` must reference a step that is in the dependencies array
-  9. **Output Paths**: Outputs must be valid filenames or paths (e.g., `report.md` or `reports/analysis.md`)
+  9. **Output Paths**: Outputs must be valid filenames or paths within the main repo (not in dot-directories). Use specific, descriptive paths that lend themselves to glob patterns, e.g., `competitive_research/competitors_list.md` or `competitive_research/[competitor_name]/research.md`. Avoid generic names like `output.md`.
   10. **Concise Instructions**: The content of the file, particularly the description, must not have excessively redundant information. It should be concise and to the point given that extra tokens will confuse the AI.
 
   <details>
@@ -538,10 +540,10 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
         - file: output.md
           from_step: previous_step_id
       outputs:
-        - filename.md               # simple filename
-        - reports/analysis.md       # path with directory
+        - competitive_research/competitors_list.md           # descriptive path
+        - competitive_research/[competitor_name]/research.md # parameterized path
         # With doc spec reference:
-        - file: report.md
+        - file: competitive_research/final_report.md
           doc_spec: .deepwork/doc_specs/report_type.md
       dependencies:
         - previous_step_id          # steps that must complete first
@@ -592,7 +594,7 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
   1. **No circular dependencies**: Step A cannot depend on Step B if Step B depends on Step A
   2. **File inputs require dependencies**: If a step uses `from_step: X`, then X must be in its dependencies
   3. **Unique step IDs**: No two steps can have the same id
-  4. **Valid file paths**: Output paths must not contain invalid characters
+  4. **Valid file paths**: Output paths must not contain invalid characters and should be in the main repo (not dot-directories)
   5. **Instructions files exist**: Each `instructions_file` path should have a corresponding file created
 
   ## Example: Complete Job Specification
@@ -627,18 +629,18 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
         - name: product_category
           description: "The product category"
       outputs:
-        - competitors_list.md
+        - competitive_research/competitors_list.md
       dependencies: []
 
     - id: research_competitors
       name: "Research Competitors"
       description: "Deep dive research on each identified competitor"
       instructions_file: steps/research_competitors.md
       inputs:
-        - file: competitors_list.md
+        - file: competitive_research/competitors_list.md
           from_step: identify_competitors
       outputs:
-        - research_notes.md
+        - competitive_research/[competitor_name]/research.md
       dependencies:
         - identify_competitors
 
@@ -647,10 +649,10 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
       description: "Strategic positioning recommendations"
       instructions_file: steps/positioning_report.md
       inputs:
-        - file: research_notes.md
+        - file: competitive_research/[competitor_name]/research.md
           from_step: research_competitors
       outputs:
-        - file: positioning_report.md
+        - file: competitive_research/positioning_report.md
           doc_spec: .deepwork/doc_specs/positioning_report.md
       dependencies:
         - research_competitors

.claude/skills/deepwork_jobs.learn/SKILL.md

@@ -50,13 +50,13 @@ hooks:
 
 ## Objective
 
-Think deeply about this task. Reflect on the current conversation to identify learnings from DeepWork job executions, improve job instructions with generalizable insights, and capture bespoke (run-specific) learnings in AGENTS.md files in the appropriate working folder.
+Think deeply about this task. Reflect on the current conversation to identify learnings from DeepWork job executions, improve job instructions with generalizable insights, and capture bespoke (run-specific) learnings in AGENTS.md files in the deepest common folder that would contain all work on the topic in the future.
 
 ## Task
 
 Analyze the conversation history to extract learnings and improvements, then apply them appropriately:
 - **Generalizable learnings** → Update job instruction files
-- **Bespoke learnings** (specific to this run) → Add to AGENTS.md in working folder
+- **Bespoke learnings** (specific to this run) → Add to AGENTS.md in the deepest common folder for the topic
 
 ### Step 1: Analyze Conversation for Job Executions
 
@@ -65,7 +65,8 @@ Analyze the conversation history to extract learnings and improvements, then app
    - Identify which jobs and steps were executed
    - Note the order of execution
 
-2. **Identify the working folder**
+2. **Identify the target folder**
+   - This should be the deepest common folder that would contain all work on the topic in the future
    - Should be clear from conversation history where work was done
    - If unclear, run `git diff` to see where changes were made on the branch
 
@@ -249,7 +250,7 @@ quality_criteria:
 The AGENTS.md file captures project-specific knowledge that helps future agent runs.
 
 1. **Determine the correct location**
-   - Place AGENTS.md in the working folder where job outputs live
+   - Place AGENTS.md in the deepest common folder that would contain all work on the topic in the future
    - This ensures the knowledge is available when working in that context
    - If uncertain, place at the project root
 
@@ -317,7 +318,7 @@ When adding entries to AGENTS.md, prefer these patterns:
 - Shared/lengthy content extracted into referenced files where appropriate
 - AGENTS.md created/updated with bespoke learnings
 - File references used instead of duplicating content
-- AGENTS.md is in the correct working folder
+- AGENTS.md is in the correct folder (the deepest common folder for the topic)
 - When all criteria are met, include `<promise>✓ Quality Criteria Met</promise>`
 
 ## Example Dialog

.claude/skills/deepwork_jobs.review_job_spec/SKILL.md

@@ -297,7 +297,7 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
   6. **Complete Steps**: Each step must have: id (lowercase_underscores), name, description, instructions_file, outputs (at least one), and dependencies array
   7. **Valid Dependencies**: Dependencies must reference existing step IDs with no circular references
   8. **Input Consistency**: File inputs with `from_step` must reference a step that is in the dependencies array
-  9. **Output Paths**: Outputs must be valid filenames or paths (e.g., `report.md` or `reports/analysis.md`)
+  9. **Output Paths**: Outputs must be valid filenames or paths within the main repo (not in dot-directories). Use specific, descriptive paths that lend themselves to glob patterns, e.g., `competitive_research/competitors_list.md` or `competitive_research/[competitor_name]/research.md`. Avoid generic names like `output.md`.
   10. **Concise Instructions**: The content of the file, particularly the description, must not have excessively redundant information. It should be concise and to the point given that extra tokens will confuse the AI.
 
   <details>
@@ -347,10 +347,10 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
         - file: output.md
           from_step: previous_step_id
       outputs:
-        - filename.md               # simple filename
-        - reports/analysis.md       # path with directory
+        - competitive_research/competitors_list.md           # descriptive path
+        - competitive_research/[competitor_name]/research.md # parameterized path
         # With doc spec reference:
-        - file: report.md
+        - file: competitive_research/final_report.md
           doc_spec: .deepwork/doc_specs/report_type.md
       dependencies:
         - previous_step_id          # steps that must complete first
@@ -401,7 +401,7 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
   1. **No circular dependencies**: Step A cannot depend on Step B if Step B depends on Step A
   2. **File inputs require dependencies**: If a step uses `from_step: X`, then X must be in its dependencies
   3. **Unique step IDs**: No two steps can have the same id
-  4. **Valid file paths**: Output paths must not contain invalid characters
+  4. **Valid file paths**: Output paths must not contain invalid characters and should be in the main repo (not dot-directories)
   5. **Instructions files exist**: Each `instructions_file` path should have a corresponding file created
 
   ## Example: Complete Job Specification
@@ -436,18 +436,18 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
         - name: product_category
           description: "The product category"
       outputs:
-        - competitors_list.md
+        - competitive_research/competitors_list.md
       dependencies: []
 
     - id: research_competitors
       name: "Research Competitors"
       description: "Deep dive research on each identified competitor"
       instructions_file: steps/research_competitors.md
       inputs:
-        - file: competitors_list.md
+        - file: competitive_research/competitors_list.md
           from_step: identify_competitors
       outputs:
-        - research_notes.md
+        - competitive_research/[competitor_name]/research.md
       dependencies:
         - identify_competitors
 
@@ -456,10 +456,10 @@ Use branch format: `deepwork/deepwork_jobs-[instance]-YYYYMMDD`
       description: "Strategic positioning recommendations"
       instructions_file: steps/positioning_report.md
       inputs:
-        - file: research_notes.md
+        - file: competitive_research/[competitor_name]/research.md
           from_step: research_competitors
       outputs:
-        - file: positioning_report.md
+        - file: competitive_research/positioning_report.md
           doc_spec: .deepwork/doc_specs/positioning_report.md
       dependencies:
         - research_competitors

.deepwork/doc_specs/job_spec.md

@@ -23,7 +23,7 @@ quality_criteria:
   - name: Input Consistency
     description: "File inputs with `from_step` must reference a step that is in the dependencies array"
   - name: Output Paths
-    description: "Outputs must be valid filenames or paths (e.g., `report.md` or `reports/analysis.md`)"
+    description: "Outputs must be valid filenames or paths within the main repo (not in dot-directories). Use specific, descriptive paths that lend themselves to glob patterns, e.g., `competitive_research/competitors_list.md` or `competitive_research/[competitor_name]/research.md`. Avoid generic names like `output.md`."
   - name: Concise Instructions
     description: "The content of the file, particularly the description, must not have excessively redundant information. It should be concise and to the point given that extra tokens will confuse the AI."
 ---
@@ -71,10 +71,10 @@ steps:
       - file: output.md
         from_step: previous_step_id
     outputs:
-      - filename.md               # simple filename
-      - reports/analysis.md       # path with directory
+      - competitive_research/competitors_list.md           # descriptive path
+      - competitive_research/[competitor_name]/research.md # parameterized path
       # With doc spec reference:
-      - file: report.md
+      - file: competitive_research/final_report.md
         doc_spec: .deepwork/doc_specs/report_type.md
     dependencies:
       - previous_step_id          # steps that must complete first
@@ -125,7 +125,7 @@ steps:
 1. **No circular dependencies**: Step A cannot depend on Step B if Step B depends on Step A
 2. **File inputs require dependencies**: If a step uses `from_step: X`, then X must be in its dependencies
 3. **Unique step IDs**: No two steps can have the same id
-4. **Valid file paths**: Output paths must not contain invalid characters
+4. **Valid file paths**: Output paths must not contain invalid characters and should be in the main repo (not dot-directories)
 5. **Instructions files exist**: Each `instructions_file` path should have a corresponding file created
 
 ## Example: Complete Job Specification
@@ -160,18 +160,18 @@ steps:
       - name: product_category
         description: "The product category"
     outputs:
-      - competitors_list.md
+      - competitive_research/competitors_list.md
     dependencies: []
 
   - id: research_competitors
     name: "Research Competitors"
     description: "Deep dive research on each identified competitor"
     instructions_file: steps/research_competitors.md
     inputs:
-      - file: competitors_list.md
+      - file: competitive_research/competitors_list.md
         from_step: identify_competitors
     outputs:
-      - research_notes.md
+      - competitive_research/[competitor_name]/research.md
     dependencies:
       - identify_competitors
 
@@ -180,10 +180,10 @@ steps:
     description: "Strategic positioning recommendations"
     instructions_file: steps/positioning_report.md
     inputs:
-      - file: research_notes.md
+      - file: competitive_research/[competitor_name]/research.md
         from_step: research_competitors
     outputs:
-      - file: positioning_report.md
+      - file: competitive_research/positioning_report.md
         doc_spec: .deepwork/doc_specs/positioning_report.md
     dependencies:
       - research_competitors

.deepwork/jobs/deepwork_jobs/doc_specs/job_spec.md

@@ -23,7 +23,7 @@ quality_criteria:
   - name: Input Consistency
     description: "File inputs with `from_step` must reference a step that is in the dependencies array"
   - name: Output Paths
-    description: "Outputs must be valid filenames or paths (e.g., `report.md` or `reports/analysis.md`)"
+    description: "Outputs must be valid filenames or paths within the main repo (not in dot-directories). Use specific, descriptive paths that lend themselves to glob patterns, e.g., `competitive_research/competitors_list.md` or `competitive_research/[competitor_name]/research.md`. Avoid generic names like `output.md`."
   - name: Concise Instructions
     description: "The content of the file, particularly the description, must not have excessively redundant information. It should be concise and to the point given that extra tokens will confuse the AI."
 ---
@@ -71,10 +71,10 @@ steps:
       - file: output.md
         from_step: previous_step_id
     outputs:
-      - filename.md               # simple filename
-      - reports/analysis.md       # path with directory
+      - competitive_research/competitors_list.md           # descriptive path
+      - competitive_research/[competitor_name]/research.md # parameterized path
       # With doc spec reference:
-      - file: report.md
+      - file: competitive_research/final_report.md
         doc_spec: .deepwork/doc_specs/report_type.md
     dependencies:
       - previous_step_id          # steps that must complete first
@@ -125,7 +125,7 @@ steps:
 1. **No circular dependencies**: Step A cannot depend on Step B if Step B depends on Step A
 2. **File inputs require dependencies**: If a step uses `from_step: X`, then X must be in its dependencies
 3. **Unique step IDs**: No two steps can have the same id
-4. **Valid file paths**: Output paths must not contain invalid characters
+4. **Valid file paths**: Output paths must not contain invalid characters and should be in the main repo (not dot-directories)
 5. **Instructions files exist**: Each `instructions_file` path should have a corresponding file created
 
 ## Example: Complete Job Specification
@@ -160,18 +160,18 @@ steps:
       - name: product_category
         description: "The product category"
     outputs:
-      - competitors_list.md
+      - competitive_research/competitors_list.md
     dependencies: []
 
   - id: research_competitors
     name: "Research Competitors"
     description: "Deep dive research on each identified competitor"
     instructions_file: steps/research_competitors.md
     inputs:
-      - file: competitors_list.md
+      - file: competitive_research/competitors_list.md
         from_step: identify_competitors
     outputs:
-      - research_notes.md
+      - competitive_research/[competitor_name]/research.md
     dependencies:
       - identify_competitors
 
@@ -180,10 +180,10 @@ steps:
     description: "Strategic positioning recommendations"
     instructions_file: steps/positioning_report.md
     inputs:
-      - file: research_notes.md
+      - file: competitive_research/[competitor_name]/research.md
         from_step: research_competitors
     outputs:
-      - file: positioning_report.md
+      - file: competitive_research/positioning_report.md
         doc_spec: .deepwork/doc_specs/positioning_report.md
     dependencies:
       - research_competitors

.deepwork/jobs/deepwork_jobs/steps/define.md

@@ -101,6 +101,8 @@ For each major phase they mentioned, ask structured questions to gather details:
    - Where should each output be saved? (filename/path)
    - Should outputs be organized in subdirectories? (e.g., `reports/`, `data/`, `drafts/`)
    - Will other steps need this output?
+
+   **Important**: Output paths should always be within the main repository directory structure, not in dot-directories like `.deepwork/`. Dot-directories are for configuration and job definitions, not for job outputs. Use paths like `research/competitors/report.md` rather than `.deepwork/outputs/report.md`.
    - **Does this output have a doc spec?** If a doc spec was created in Step 1.6/1.7, reference it for the appropriate output
 
 4. **Step Dependencies**