diff --git a/docs/how-to/customize-bmad.md b/docs/how-to/customize-bmad.md
index ea05ba7ca..d0986e4e0 100644
--- a/docs/how-to/customize-bmad.md
+++ b/docs/how-to/customize-bmad.md
@@ -215,7 +215,7 @@ python3 {project-root}/_bmad/scripts/resolve_customization.py \
   --key agent
 ```
 
-**Requirements**: Python 3.11+ (earlier versions don't include `tomllib`). No `pip install`, no `uv`, no virtualenv. macOS 13+, Ubuntu 22.04+, Debian 12+, and Fedora 37+ all ship 3.11 or newer.
+**Requirements**: Python 3.11+ (earlier versions don't include `tomllib`). No `pip install`, no `uv`, no virtualenv. Check with `python3 --version` — some common platforms (macOS without Homebrew, Ubuntu 22.04) default `python3` to 3.10 or earlier even when 3.11+ is available to install separately.
 
 `--skill` points at the skill's installed directory (where `customize.toml` lives). The skill name is derived from the directory's basename, and the script looks up `_bmad/custom/{skill-name}.toml` and `{skill-name}.user.toml` automatically.
 
diff --git a/src/bmm-skills/1-analysis/bmad-agent-analyst/SKILL.md b/src/bmm-skills/1-analysis/bmad-agent-analyst/SKILL.md
index 2eba1b18f..4653171df 100644
--- a/src/bmm-skills/1-analysis/bmad-agent-analyst/SKILL.md
+++ b/src/bmm-skills/1-analysis/bmad-agent-analyst/SKILL.md
@@ -22,13 +22,13 @@ You are Mary, the Business Analyst. You bring deep expertise in market research,
 
 Run: `python3 {project-root}/_bmad/scripts/resolve_customization.py --skill {skill-root} --key agent`
 
-**If the script fails**, resolve the `agent` block yourself by merging these three files in priority order (later wins):
+**If the script fails**, resolve the `agent` block yourself by reading these three files in base → team → user order and applying the same structural merge rules as the resolver:
 
 1. `{skill-root}/customize.toml` — defaults
 2. `{project-root}/_bmad/custom/{skill-name}.toml` — team overrides
 3. `{project-root}/_bmad/custom/{skill-name}.user.toml` — personal overrides
 
-Any missing file is skipped.
+Any missing file is skipped. Scalars override, tables deep-merge, arrays of tables keyed by `code` or `id` replace matching entries and append new entries, and all other arrays append.
 
 ### Step 2: Execute Prepend Steps
 
diff --git a/src/bmm-skills/1-analysis/bmad-agent-tech-writer/SKILL.md b/src/bmm-skills/1-analysis/bmad-agent-tech-writer/SKILL.md
index ea642c3a2..ff6430d93 100644
--- a/src/bmm-skills/1-analysis/bmad-agent-tech-writer/SKILL.md
+++ b/src/bmm-skills/1-analysis/bmad-agent-tech-writer/SKILL.md
@@ -22,13 +22,13 @@ You are Paige, the Technical Writer. You transform complex concepts into accessi
 
 Run: `python3 {project-root}/_bmad/scripts/resolve_customization.py --skill {skill-root} --key agent`
 
-**If the script fails**, resolve the `agent` block yourself by merging these three files in priority order (later wins):
+**If the script fails**, resolve the `agent` block yourself by reading these three files in base → team → user order and applying the same structural merge rules as the resolver:
 
 1. `{skill-root}/customize.toml` — defaults
 2. `{project-root}/_bmad/custom/{skill-name}.toml` — team overrides
 3. `{project-root}/_bmad/custom/{skill-name}.user.toml` — personal overrides
 
-Any missing file is skipped.
+Any missing file is skipped. Scalars override, tables deep-merge, arrays of tables keyed by `code` or `id` replace matching entries and append new entries, and all other arrays append.
 
 ### Step 2: Execute Prepend Steps
 
diff --git a/src/bmm-skills/1-analysis/bmad-product-brief/SKILL.md b/src/bmm-skills/1-analysis/bmad-product-brief/SKILL.md
index 8ae6c2be4..8d697259e 100644
--- a/src/bmm-skills/1-analysis/bmad-product-brief/SKILL.md
+++ b/src/bmm-skills/1-analysis/bmad-product-brief/SKILL.md
@@ -41,13 +41,13 @@ Check activation context immediately:
 
 Run: `python3 {project-root}/_bmad/scripts/resolve_customization.py --skill {skill-root} --key workflow`
 
-**If the script fails**, resolve the `workflow` block yourself by merging these three files in priority order (later wins):
+**If the script fails**, resolve the `workflow` block yourself by reading these three files in base → team → user order and applying the same structural merge rules as the resolver:
 
 1. `{skill-root}/customize.toml` — defaults
 2. `{project-root}/_bmad/custom/{skill-name}.toml` — team overrides
 3. `{project-root}/_bmad/custom/{skill-name}.user.toml` — personal overrides
 
-Any missing file is skipped.
+Any missing file is skipped. Scalars override, tables deep-merge, arrays of tables keyed by `code` or `id` replace matching entries and append new entries, and all other arrays append.
 
 ### Step 2: Execute Prepend Steps
 
@@ -68,7 +68,7 @@ Load config from `{project-root}/_bmad/bmm/config.yaml` and resolve:
 
 ### Step 5: Greet the User
 
-Greet `{user_name}` if you have not already, speaking in `{communication_language}`.
+If `{mode}` is not `autonomous`, greet `{user_name}` (if you have not already), speaking in `{communication_language}`. In autonomous mode, skip the greeting — no conversational output should precede the generated artifact.
 
 ### Step 6: Execute Append Steps
 
diff --git a/src/bmm-skills/2-plan-workflows/bmad-agent-pm/SKILL.md b/src/bmm-skills/2-plan-workflows/bmad-agent-pm/SKILL.md
index a4ef415af..693072603 100644
--- a/src/bmm-skills/2-plan-workflows/bmad-agent-pm/SKILL.md
+++ b/src/bmm-skills/2-plan-workflows/bmad-agent-pm/SKILL.md
@@ -22,13 +22,13 @@ You are John, the Product Manager. You drive PRD creation through user interview
 
 Run: `python3 {project-root}/_bmad/scripts/resolve_customization.py --skill {skill-root} --key agent`
 
-**If the script fails**, resolve the `agent` block yourself by merging these three files in priority order (later wins):
+**If the script fails**, resolve the `agent` block yourself by reading these three files in base → team → user order and applying the same structural merge rules as the resolver:
 
 1. `{skill-root}/customize.toml` — defaults
 2. `{project-root}/_bmad/custom/{skill-name}.toml` — team overrides
 3. `{project-root}/_bmad/custom/{skill-name}.user.toml` — personal overrides
 
-Any missing file is skipped.
+Any missing file is skipped. Scalars override, tables deep-merge, arrays of tables keyed by `code` or `id` replace matching entries and append new entries, and all other arrays append.
 
 ### Step 2: Execute Prepend Steps
 
diff --git a/src/bmm-skills/2-plan-workflows/bmad-agent-ux-designer/SKILL.md b/src/bmm-skills/2-plan-workflows/bmad-agent-ux-designer/SKILL.md
index 56902d3e9..cb261c3fb 100644
--- a/src/bmm-skills/2-plan-workflows/bmad-agent-ux-designer/SKILL.md
+++ b/src/bmm-skills/2-plan-workflows/bmad-agent-ux-designer/SKILL.md
@@ -22,13 +22,13 @@ You are Sally, the UX Designer. You translate user needs into interaction design
 
 Run: `python3 {project-root}/_bmad/scripts/resolve_customization.py --skill {skill-root} --key agent`
 
-**If the script fails**, resolve the `agent` block yourself by merging these three files in priority order (later wins):
+**If the script fails**, resolve the `agent` block yourself by reading these three files in base → team → user order and applying the same structural merge rules as the resolver:
 
 1. `{skill-root}/customize.toml` — defaults
 2. `{project-root}/_bmad/custom/{skill-name}.toml` — team overrides
 3. `{project-root}/_bmad/custom/{skill-name}.user.toml` — personal overrides
 
-Any missing file is skipped.
+Any missing file is skipped. Scalars override, tables deep-merge, arrays of tables keyed by `code` or `id` replace matching entries and append new entries, and all other arrays append.
 
 ### Step 2: Execute Prepend Steps
 
diff --git a/src/bmm-skills/3-solutioning/bmad-agent-architect/SKILL.md b/src/bmm-skills/3-solutioning/bmad-agent-architect/SKILL.md
index 07bd26ca4..1650aee09 100644
--- a/src/bmm-skills/3-solutioning/bmad-agent-architect/SKILL.md
+++ b/src/bmm-skills/3-solutioning/bmad-agent-architect/SKILL.md
@@ -22,13 +22,13 @@ You are Winston, the System Architect. You turn product requirements and UX into
 
 Run: `python3 {project-root}/_bmad/scripts/resolve_customization.py --skill {skill-root} --key agent`
 
-**If the script fails**, resolve the `agent` block yourself by merging these three files in priority order (later wins):
+**If the script fails**, resolve the `agent` block yourself by reading these three files in base → team → user order and applying the same structural merge rules as the resolver:
 
 1. `{skill-root}/customize.toml` — defaults
 2. `{project-root}/_bmad/custom/{skill-name}.toml` — team overrides
 3. `{project-root}/_bmad/custom/{skill-name}.user.toml` — personal overrides
 
-Any missing file is skipped.
+Any missing file is skipped. Scalars override, tables deep-merge, arrays of tables keyed by `code` or `id` replace matching entries and append new entries, and all other arrays append.
 
 ### Step 2: Execute Prepend Steps
 
diff --git a/src/bmm-skills/4-implementation/bmad-agent-dev/SKILL.md b/src/bmm-skills/4-implementation/bmad-agent-dev/SKILL.md
index 59e5bf8a5..95a3b9594 100644
--- a/src/bmm-skills/4-implementation/bmad-agent-dev/SKILL.md
+++ b/src/bmm-skills/4-implementation/bmad-agent-dev/SKILL.md
@@ -22,13 +22,13 @@ You are Amelia, the Senior Software Engineer. You execute approved stories with
 
 Run: `python3 {project-root}/_bmad/scripts/resolve_customization.py --skill {skill-root} --key agent`
 
-**If the script fails**, resolve the `agent` block yourself by merging these three files in priority order (later wins):
+**If the script fails**, resolve the `agent` block yourself by reading these three files in base → team → user order and applying the same structural merge rules as the resolver:
 
 1. `{skill-root}/customize.toml` — defaults
 2. `{project-root}/_bmad/custom/{skill-name}.toml` — team overrides
 3. `{project-root}/_bmad/custom/{skill-name}.user.toml` — personal overrides
 
-Any missing file is skipped.
+Any missing file is skipped. Scalars override, tables deep-merge, arrays of tables keyed by `code` or `id` replace matching entries and append new entries, and all other arrays append.
 
 ### Step 2: Execute Prepend Steps