diff --git a/src/glide/assets/config.yml b/src/glide/assets/config.yml
index d953f4f..df44767 100644
--- a/src/glide/assets/config.yml
+++ b/src/glide/assets/config.yml
@@ -1,468 +1,92 @@
-# glide's default configuration is specified in this file. 
-# Variable formatting mostly follows national gdlier DAC netCDF format version 2
-# https://ioos.github.io/glider-dac/ngdac-netcdf-file-format-version-2
-# This file is self-documenting in the sense that it is liberally commented.
-# The comments provide pointers and tips for defining the configuration.
-
-# Dashes (---) indicate separate yaml documents. They are important. 
-# The ordering of documents is important. 
+# glide user configuration
+# 
+# This file configures your glider deployment. Core variables are defined
+# in the package and cannot be removed, but their QC parameters can be
+# adjusted here.
+#
+# For documentation, see: https://github.com/OSUGliders/glide
 
---- ### PART 1 GLOBAL CONFIGURATION
+--- ### DEPLOYMENT INFO
 
-# Edit the name for your deployment
-trajectory: 
+# Edit the trajectory name for your deployment (required)
+trajectory:
   name: YYYYMMDD_gliderSN
-  attributes: # Don't change the attributes, they are required by IOOS
+  attributes:
     cf_role: trajectory_id
     comment: "A trajectory is a single deployment of a glider and may span multiple data files."
-    long_name: "Trajectory/Deployment Name"
+    long_name: Trajectory/Deployment Name
 
-# Add CF standard global attributes here
+# Global netCDF attributes (CF standard)
 netcdf_attributes:
   title: Example Slocum glider dataset generated by the python package glide.
   comment: glide is developed by the OSU glider group at https://github.com/OSUGliders/glide
   conventions: "CF-1.6, Unidata Dataset Discovery v1.0"
 
---- ### PART 2 VARIABLE DEFINITIONS, QC CONTROLS, AND METADATA
-
-# This part defines variables. The first item in the hierarchy is the variable name as
-# we want it outputted in the file. The next level in the heirarchy defines how we
-# want to process the variable. Note that some of the CF attributes are used to tune QC.
-# Specifically, the valid_min and valid_max attributes are used to threshold data when
-# they are defined.
-#
-# variable_name:
-#   source: Slocum name from masterdata
-#   track_qc: True/False
-#   conversion: must match a function in convert.py
-#   interpolate_missing: True/False
-#   max_gap: Maximum interpolation gap in seconds
-#   drop_from_l2: True/False
-#   dtype: numpy type code, e.g. f4, f8 for float, double
-#   CF:
-#     standard_name: ...
-
-# TIME VARIABLES
-
-time: # This is the name the we want
-  # This list of sources can only be done for variables that do not appear in the same file
-  # because we are essentially mapping one variable name, time, to two other variable names.
-  source: ["m_present_time", "sci_m_present_time"]
-  track_qc: True
-  CF: # CF attributes here
-    long_name: Time
-    standard_name: time
-    calendar: gregorian
-    units: seconds since 1970-01-01T00:00:00Z
-    axis: T
-    observation_type: "measured"
-    valid_min: 2000-01-01T00:00:00  # pyyaml automatically converts timestamps to datetime.datetime objects
-    valid_max: 2040-01-01T00:00:00
-
-# FLIGHT COMPUTER VARIABLES
-
-lat: # This is the name that we want
-  source: m_lat  # This is the name that Slocum gliders use
-  conversion: dpm_to_dd  # Function applied to convert data units
-  interpolate_missing: True  # Interpolating nan values
-  max_gap: 600  # Max gap in seconds over which to interpolate nan values
-  track_qc: True  # Whether to keep track of quality control
-  dtype: f4
-  CF: 
-    long_name: Latitude
-    standard_name: latitude
-    units: degrees_north
-    axis: Y
-    comment: "Estimated between surface fixes"
-    observation_type: measured
-    platform: platform
-    reference: WGS84
-    valid_max: 90.0
-    valid_min: -90.0
-    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
-
-lon:
-  source: m_lon
-  conversion: dpm_to_dd
-  interpolate_missing: True
-  max_gap: 600
-  track_qc: True
-  dtype: f4
-  CF:
-    long_name: Longitude
-    standard_name: longitude
-    units: degrees_east
-    axis: X
-    comment: "Estimated between surface fixes"
-    observation_type: measured
-    platform: platform
-    reference: WGS84
-    valid_max: 180.0
-    valid_min: -180.0
-    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
-
-m_gps_lat:
-  source: m_gps_lat
-  conversion: dpm_to_dd
-  drop_from_l2: True  # Not included into l2 dataset if true
-  CF: 
-    long_name: Latitude
-    standard_name: latitude
-    units: degrees_north
-    axis: Y
-    comment: "Surface fixes"
-    observation_type: measured
-    platform: platform
-    reference: WGS84
-    valid_max: 90.0
-    valid_min: -90.0
-    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
-
-m_gps_lon:
-  source: m_gps_lon
-  conversion: dpm_to_dd
-  drop_from_l2: True
-  CF:
-    long_name: Longitude
-    standard_name: longitude
-    units: degrees_east
-    axis: X
-    comment: "Surface fixes"
-    observation_type: measured
-    platform: platform
-    reference: WGS84
-    valid_max: 180.0
-    valid_min: -180.0
-    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
-
-u:
-  dtype: f4
-  CF:
-    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
-    long_name: "Depth-Averaged Eastward Sea Water Velocity"
-    observation_type: "calculated"
-    platform: "platform"
-    source_sensor: "m_water_vx"
-    standard_name: "eastward_sea_water_velocity"
-    units: "m s-1"
-    valid_max: 10.
-    valid_min: -10.
-
-v:
-  dtype: f4
-  CF:
-    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
-    long_name: "Depth-Averaged Northward Sea Water Velocity"
-    observation_type: "calculated"
-    platform: "platform"
-    source_sensor: "m_water_vy"
-    standard_name: "northward_sea_water_velocity"
-    units: "m s-1"
-    valid_max: 10.
-    valid_min: -10.
-
-time_uv:
-  CF:
-    calendar: "gregorian"
-    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
-    long_name: "Depth-Averaged Time"
-    observation_type: "calculated"
-    source_sensor: "m_present_time"
-    standard_name: "time"
-    units: "seconds since 1970-01-01T00:00:00Z"
-
-lat_uv:
-  dtype: f4
-  CF:
-    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
-    long_name: "Depth-Averaged Latitude"
-    observation_type: "calculated"
-    platform: "platform"
-    source_sensor: "m_gps_lat"
-    standard_name: "latitude"
-    units: "degrees_north"
-    valid_max: 90.
-    valid_min: -90.
-
-lon_uv:
-  dtype: f4
-  CF:
-    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
-    long_name: "Depth-Averaged Longitude"
-    observation_type: "calculated"
-    platform: "platform"
-    source_sensor: "m_gps_lon"
-    standard_name: "longitude"
-    units: "degrees_east"
-    valid_max: 180.
-    valid_min: -180.
-
-heading:
-  source: m_heading
-  conversion: rad_to_deg
-  interpolate_missing: True
-  dtype: f4
-  CF:
-    long_name: Heading
-    standard_name: platform_orientation
-    units: degrees
-    observation_type: measured
-    valid_max: 360.0
-    valid_min: 0.0
-
-pitch: 
-  source: m_pitch
-  conversion: rad_to_deg
-  interpolate_missing: True
-  dtype: f4
-  CF:
-    long_name: Pitch
-    standard_name: platform_pitch_fore_up
-    units: degrees
-    observation_type: measured
-    valid_max: 180.0
-    valid_min: -180.0
+--- ### OPTIONAL VARIABLE SUITES
 
-roll:
-  source: m_roll 
-  conversion: rad_to_deg
-  interpolate_missing: True
-  dtype: f4
-  CF:
-    long_name: Roll
-    standard_name: platform_roll_starboard_down
-    units: degrees
-    observation_type: measured
-    valid_max: 180.0
-    valid_min: -180.0
+# Toggle optional variable groups on/off
+include:
+  flight: true   # fin, battpos, heading, ballast_pumped
+  thermo: true    # salinity, density, rho0, SA, CT, N2, depth, z
 
-m_depth:
-  source: m_depth
-  drop_from_l2: True
-  CF:
-    long_name: Depth
-    standard_name: depth
-    units: m
-    valid_min: 0.0
-    valid_max: 2000.0
-    positive: "down"
-    reference_datum: "sea-surface"
-    instrument: "instrument_ctd"
-    observation_type: "measured"
+--- ### QC PARAMETER OVERRIDES
 
-# m_fin: 
-#   source: m_fin
-#   conversion: rad_to_deg
-#   interpolate_missing: True
-#   dtype: f4
-#   CF:
-#     long_name: Fin angle
-#     units: degrees
-
-# m_battpos:
-#   source: m_battpos
-#   interpolate_missing: True
-#   dtype: f4
-#   CF:
-#     long_name: Battery position
-#     units: inches
-    
-# SCIENCE COMPUTER VARIABLES
-
-pressure: 
-  source: sci_water_pressure
-  conversion: bar_to_dbar
-  interpolate_missing: True
-  track_qc: True
-  dtype: f4
-  CF: 
-    long_name: Pressure
-    standard_name: sea_water_pressure
-    units: dbar
-    valid_min: 0.0
-    valid_max: 2000.0
-    positive: "down"
-    reference_datum: "sea-surface"
-    instrument: "instrument_ctd"
-    observation_type: "measured"
-    accuracy: 1.0
-    precision: 2.0
-    resolution: 0.02
-    comment: "ctd pressure sensor"
-
-conductivity:
-  source: sci_water_cond
-  interpolate_missing: True
-  track_qc: True
-  dtype: f4
-  CF:
-    long_name: Conductivity
-    standard_name: sea_water_electrical_conductivity
-    units: S m-1  # Not converted to mS cm-1 becase we need S m-1 for glider DAC
-    instrument: instrument_ctd
-    valid_min: 0.1
-    valid_max: 10.
-    observation_type: "measured"
-    accuracy: 0.0003
-    precision: 0.0001
-    resolution: 0.00002
-
-temperature:
-  source: sci_water_temp
-  interpolate_missing: True
-  track_qc: True
-  dtype: f4
-  CF:
-    long_name: Temperature
-    standard_name: sea_water_temperature
-    units: celsius
-    instrument: instrument_ctd
-    valid_min: -5.0
-    valid_max: 50.0
-    observation_type: "measured"
-    accuracy: 0.002
-    precision: 0.001
-    resolution: 0.0002
-
-# CALCULATED VARIABLES
-
-salinity:
-  track_qc: True
-  dtype: f4
-  CF:
-    # accuracy:
-    instrument: instrument_ctd
-    long_name: Salinity
-    observation_type: calculated
-    platform: platform
-    # precision:
-    # resolution:
-    standard_name: sea_water_practical_salinity
-    units: 1
-    valid_max: 40.0
-    valid_min: 0.0
-
-density:
-  track_qc: True
-  dtype: f4
-  CF: 
-    # accuracy:
-    instrument: instrument_ctd
-    long_name: Density
-    observation_type: calculated
-    platform: platform
-    # precision:
-    # resolution:
-    standard_name: sea_water_density
-    units: kg m-3
-    valid_max: 1040.0
-    valid_min: 1015.0
-
-rho0:
-  track_qc: True
-  dtype: f4
-  CF: 
-    # accuracy:
-    instrument: instrument_ctd
-    long_name: Potential density
-    observation_type: calculated
-    platform: platform
-    reference_pressure: 0
-    # precision:
-    # resolution:
-    standard_name: sea_water_potential_density
-    units: kg m-3
-    valid_max: 1040.0
-    valid_min: 1015.0
-
-SA:
-  track_qc: True
-  dtype: f4
-  CF:
-    # accuracy:
-    instrument: instrument_ctd
-    long_name: Absolute salinity
-    observation_type: calculated
-    platform: platform
-    # precision:
-    # resolution:
-    standard_name: sea_water_absolute_salinity
-    units: g kg-1
-    valid_max: 40.0
-    valid_min: 0.0
-
-CT:
-  track_qc: True
-  dtype: f4
-  CF:
-    long_name: Conservative temperature
-    standard_name: sea_water_conservative_temperature
-    units: celsius
-    instrument: instrument_ctd
-    valid_min: -5.0
-    valid_max: 50.0
-    observation_type: calculated
-    # accuracy: 0.002
-    # precision: 0.001
-    # resolution: 0.0002
-
-N2:
-  track_qc: True
-  dtype: f4
-  CF:
-    long_name: Buoyancy frequency squared
-    standard_name: square_of_brunt_vaisala_frequency_in_sea_water
-    units: s-2
-    observations_type: calculated
-
-depth:
-  track_qc: True
-  dtype: f4
-  CF:
-    long_name: Depth
-    standard_name: depth
-    units: m
-    valid_min: 0.0
-    valid_max: 2000.0
-    positive: "down"
-    reference_datum: "sea-surface"
-    instrument: "instrument_ctd"
-    observation_type: "calculated"
-
-z:
-  track_qc: True
-  dtype: f4
-  CF:
-    long_name: Height
-    standard_name: height
-    units: m
-    valid_min: -2000.0
-    valid_max: 0.0
-    positive: "up"
-    reference_datum: "sea-surface"
-    instrument: "instrument_ctd"
-    observation_type: "calculated"
-
-# ASSIMILATED VARIABLES
-
-e_1:
-  CF: 
-    long_name: TKE dissipation rate
-    standard_name: specific_turbulent_kinetic_energy_dissipation_in_sea_water
-    comment: Estimated using shear probe 1
-    units: W kg-1
-    valid_min: 0.0
-    valid_max: 0.001
-    instrument: "instrument_microrider"
-    observation_type: "calculated"
-
-e_2: 
-  CF: 
-    long_name: TKE dissipation rate
-    standard_name: specific_turbulent_kinetic_energy_dissipation_in_sea_water
-    comment: Estimated using shear probe 2
-    units: W kg-1
-    valid_min: 0.0
-    valid_max: 0.001
-    instrument: "instrument_microrider"
-    observation_type: "calculated"
\ No newline at end of file
+# Override QC parameters for core variables on a per-deployment basis.
+# Only these parameters can be changed: valid_min, valid_max, max_gap, interpolate_missing
+# Example:
+#
+# qc:
+#   temperature:
+#     valid_min: -2.0  
+#     valid_max: 15.0
+#   lat:
+#     max_gap: 900
+#   pressure:
+#     valid_max: 1200.0
+
+qc: {}
+
+--- ### L1 EXTRA VARIABLES
+
+# Additional variables to extract from raw Slocum data during L1->L2 processing.
+# These require a 'source' field matching the Slocum variable name.
+# Example:
+#
+# l1_variables:
+#   fin:  # Note that this variable is already included in the flight suite
+#     source: m_fin
+#     conversion: rad_to_deg
+#     dtype: f4
+#     CF:
+#       long_name: Fin angle
+#       units: degrees
+
+l1_variables: {}
+
+--- ### MERGED VARIABLES
+
+# Variables to be assimilated from external processing (e.g., microstructure).
+# These are used in higher-level processing and do not have a 'source' field.
+
+merged_variables:
+  e_1:
+    CF:
+      long_name: TKE dissipation rate
+      standard_name: specific_turbulent_kinetic_energy_dissipation_in_sea_water
+      comment: Estimated using shear probe 1
+      units: W kg-1
+      valid_min: 0.0
+      valid_max: 0.001
+      instrument: instrument_microrider
+      observation_type: calculated
+
+  e_2:
+    CF:
+      long_name: TKE dissipation rate
+      standard_name: specific_turbulent_kinetic_energy_dissipation_in_sea_water
+      comment: Estimated using shear probe 2
+      units: W kg-1
+      valid_min: 0.0
+      valid_max: 0.001
+      instrument: instrument_microrider
+      observation_type: calculated
\ No newline at end of file
diff --git a/src/glide/assets/core.yml b/src/glide/assets/core.yml
new file mode 100644
index 0000000..076ed94
--- /dev/null
+++ b/src/glide/assets/core.yml
@@ -0,0 +1,421 @@
+# Core variable definitions for glide
+# This file is bundled with the package and should not be edited by users.
+# Variable formatting follows IOOS national glider DAC netCDF format version 2
+# https://ioos.github.io/glider-dac/ngdac-netcdf-file-format-version-2
+
+# Dashes (---) indicate separate yaml documents.
+
+--- ### CORE VARIABLES (always extracted)
+
+time:
+  source: ["m_present_time", "sci_m_present_time"]
+  track_qc: True
+  CF:
+    long_name: Time
+    standard_name: time
+    calendar: gregorian
+    units: seconds since 1970-01-01T00:00:00Z
+    axis: T
+    observation_type: measured
+    valid_min: 2000-01-01T00:00:00
+    valid_max: 2040-01-01T00:00:00
+
+lat:
+  source: m_lat
+  conversion: dpm_to_dd
+  interpolate_missing: True
+  max_gap: 600
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Latitude
+    standard_name: latitude
+    units: degrees_north
+    axis: Y
+    comment: "Estimated between surface fixes"
+    observation_type: measured
+    platform: platform
+    reference: WGS84
+    valid_max: 90.0
+    valid_min: -90.0
+    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
+
+lon:
+  source: m_lon
+  conversion: dpm_to_dd
+  interpolate_missing: True
+  max_gap: 600
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Longitude
+    standard_name: longitude
+    units: degrees_east
+    axis: X
+    comment: "Estimated between surface fixes"
+    observation_type: measured
+    platform: platform
+    reference: WGS84
+    valid_max: 180.0
+    valid_min: -180.0
+    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
+
+m_gps_lat:
+  source: m_gps_lat
+  conversion: dpm_to_dd
+  drop_from_l2: True
+  CF:
+    long_name: Latitude
+    standard_name: latitude
+    units: degrees_north
+    axis: Y
+    comment: "Surface fixes"
+    observation_type: measured
+    platform: platform
+    reference: WGS84
+    valid_max: 90.0
+    valid_min: -90.0
+    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
+
+m_gps_lon:
+  source: m_gps_lon
+  conversion: dpm_to_dd
+  drop_from_l2: True
+  CF:
+    long_name: Longitude
+    standard_name: longitude
+    units: degrees_east
+    axis: X
+    comment: "Surface fixes"
+    observation_type: measured
+    platform: platform
+    reference: WGS84
+    valid_max: 180.0
+    valid_min: -180.0
+    coordinate_reference_frame: urn:ogc:crs:EPSG::4326
+
+m_depth:
+  source: m_depth
+  drop_from_l2: True
+  CF:
+    long_name: Depth
+    standard_name: depth
+    units: m
+    valid_min: 0.0
+    valid_max: 2000.0
+    positive: down
+    reference_datum: sea-surface
+    instrument: instrument_ctd
+    observation_type: measured
+
+pressure:
+  source: sci_water_pressure
+  conversion: bar_to_dbar
+  interpolate_missing: True
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Pressure
+    standard_name: sea_water_pressure
+    units: dbar
+    valid_min: 0.0
+    valid_max: 2000.0
+    positive: down
+    reference_datum: sea-surface
+    instrument: instrument_ctd
+    observation_type: measured
+    accuracy: 1.0
+    precision: 2.0
+    resolution: 0.02
+    comment: "ctd pressure sensor"
+
+conductivity:
+  source: sci_water_cond
+  interpolate_missing: True
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Conductivity
+    standard_name: sea_water_electrical_conductivity
+    units: S m-1
+    instrument: instrument_ctd
+    valid_min: 0.1
+    valid_max: 10.0
+    observation_type: measured
+    accuracy: 0.0003
+    precision: 0.0001
+    resolution: 0.00002
+
+temperature:
+  source: sci_water_temp
+  interpolate_missing: True
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Temperature
+    standard_name: sea_water_temperature
+    units: celsius
+    instrument: instrument_ctd
+    valid_min: -5.0
+    valid_max: 50.0
+    observation_type: measured
+    accuracy: 0.002
+    precision: 0.001
+    resolution: 0.0002
+
+# Core flight
+
+pitch:
+  source: m_pitch
+  conversion: rad_to_deg
+  interpolate_missing: True
+  dtype: f4
+  CF:
+    long_name: Pitch
+    standard_name: platform_pitch_fore_up
+    units: degrees
+    observation_type: measured
+    valid_max: 180.0
+    valid_min: -180.0
+
+roll:
+  source: m_roll
+  conversion: rad_to_deg
+  interpolate_missing: True
+  dtype: f4
+  CF:
+    long_name: Roll
+    standard_name: platform_roll_starboard_down
+    units: degrees
+    observation_type: measured
+    valid_max: 180.0
+    valid_min: -180.0
+
+# Velocity variables (on time_uv dimension)
+
+u:
+  dtype: f4
+  CF:
+    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
+    long_name: Depth-Averaged Eastward Sea Water Velocity
+    observation_type: calculated
+    platform: platform
+    source_sensor: m_water_vx
+    standard_name: eastward_sea_water_velocity
+    units: m s-1
+    valid_max: 10.0
+    valid_min: -10.0
+
+v:
+  dtype: f4
+  CF:
+    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
+    long_name: Depth-Averaged Northward Sea Water Velocity
+    observation_type: calculated
+    platform: platform
+    source_sensor: m_water_vy
+    standard_name: northward_sea_water_velocity
+    units: m s-1
+    valid_max: 10.0
+    valid_min: -10.0
+
+time_uv:
+  CF:
+    calendar: gregorian
+    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
+    long_name: Depth-Averaged Time
+    observation_type: calculated
+    source_sensor: m_present_time
+    standard_name: time
+    units: seconds since 1970-01-01T00:00:00Z
+
+lat_uv:
+  dtype: f4
+  CF:
+    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
+    long_name: Depth-Averaged Latitude
+    observation_type: calculated
+    platform: platform
+    source_sensor: m_gps_lat
+    standard_name: latitude
+    units: degrees_north
+    valid_max: 90.0
+    valid_min: -90.0
+
+lon_uv:
+  dtype: f4
+  CF:
+    comment: "The depth-averaged current is an estimate of the net current measured while the glider is underwater. The value is calculated over the entire underwater segment, which may consist of 1 or more dives."
+    long_name: Depth-Averaged Longitude
+    observation_type: calculated
+    platform: platform
+    source_sensor: m_gps_lon
+    standard_name: longitude
+    units: degrees_east
+    valid_max: 180.0
+    valid_min: -180.0
+
+# Profile identification variables
+
+dive_id:
+  dtype: i4
+  CF:
+    long_name: Dive ID
+    comment: "Unique identifier for each dive profile, starting from 0. -1 indicates no dive."
+
+climb_id:
+  dtype: i4
+  CF:
+    long_name: Climb ID
+    comment: "Unique identifier for each climb profile, starting from 0. -1 indicates no climb."
+
+state:
+  dtype: i1
+  CF:
+    long_name: Glider State
+    comment: "Glider state: -1=unknown, 0=surface, 1=dive, 2=climb"
+    flag_values: [-1, 0, 1, 2]
+    flag_meanings: "unknown surface dive climb"
+
+--- ### OPTIONAL SUITE: flight
+
+heading:
+  source: m_heading
+  conversion: rad_to_deg
+  interpolate_missing: True
+  dtype: f4
+  CF:
+    long_name: Heading
+    standard_name: platform_orientation
+    units: degrees
+    observation_type: measured
+    valid_max: 360.0
+    valid_min: 0.0
+
+battpos:
+  source: m_battpos
+  interpolate_missing: true
+  dtype: f4
+  CF:
+    long_name: Battery position
+    units: inches
+
+fin:
+  source: m_fin
+  conversion: rad_to_deg
+  dtype: f4
+  CF:
+    long_name: Fin angle
+    units: degrees
+
+ballast_pumped:
+  source: m_de_oil_vol
+  dtype: f4
+  CF:
+    long_name: Ballast pumped
+    units: cm^3
+    observation_type: measured
+
+--- ### OPTIONAL SUITE: thermo
+
+salinity:
+  track_qc: True
+  dtype: f4
+  CF:
+    instrument: instrument_ctd
+    long_name: Salinity
+    observation_type: calculated
+    platform: platform
+    standard_name: sea_water_practical_salinity
+    units: "1"
+    valid_max: 40.0
+    valid_min: 0.0
+
+density:
+  track_qc: True
+  dtype: f4
+  CF:
+    instrument: instrument_ctd
+    long_name: Density
+    observation_type: calculated
+    platform: platform
+    standard_name: sea_water_density
+    units: kg m-3
+    valid_max: 1040.0
+    valid_min: 1015.0
+
+rho0:
+  track_qc: True
+  dtype: f4
+  CF:
+    instrument: instrument_ctd
+    long_name: Potential density
+    observation_type: calculated
+    platform: platform
+    reference_pressure: 0
+    standard_name: sea_water_potential_density
+    units: kg m-3
+    valid_max: 1040.0
+    valid_min: 1015.0
+
+SA:
+  track_qc: True
+  dtype: f4
+  CF:
+    instrument: instrument_ctd
+    long_name: Absolute salinity
+    observation_type: calculated
+    platform: platform
+    standard_name: sea_water_absolute_salinity
+    units: g kg-1
+    valid_max: 40.0
+    valid_min: 0.0
+
+CT:
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Conservative temperature
+    standard_name: sea_water_conservative_temperature
+    units: celsius
+    instrument: instrument_ctd
+    valid_min: -5.0
+    valid_max: 50.0
+    observation_type: calculated
+
+N2:
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Buoyancy frequency squared
+    standard_name: square_of_brunt_vaisala_frequency_in_sea_water
+    units: s-2
+    observation_type: calculated
+
+depth:
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Depth
+    standard_name: depth
+    units: m
+    valid_min: 0.0
+    valid_max: 2000.0
+    positive: down
+    reference_datum: sea-surface
+    instrument: instrument_ctd
+    observation_type: calculated
+
+z:
+  track_qc: True
+  dtype: f4
+  CF:
+    long_name: Height
+    standard_name: height
+    units: m
+    valid_min: -2000.0
+    valid_max: 0.0
+    positive: up
+    reference_datum: sea-surface
+    instrument: instrument_ctd
+    observation_type: calculated
diff --git a/src/glide/config.py b/src/glide/config.py
index 32bbe1d..2deaef0 100644
--- a/src/glide/config.py
+++ b/src/glide/config.py
@@ -1,5 +1,6 @@
 # Functions for handling the configuration file
 
+import copy
 import logging
 from datetime import datetime, timezone
 
@@ -14,11 +15,115 @@ def _ensure_utc(dt: datetime) -> datetime:
     return dt.replace(tzinfo=timezone.utc)
 
 
+def _deep_merge(base: dict, override: dict) -> dict:
+    """Deep merge override into base, returning a new dict."""
+    result = copy.deepcopy(base)
+    for key, value in override.items():
+        if key in result and isinstance(result[key], dict) and isinstance(value, dict):
+            result[key] = _deep_merge(result[key], value)
+        else:
+            result[key] = copy.deepcopy(value)
+    return result
+
+
+def _load_core() -> tuple[dict, dict, dict]:
+    """Load core variable definitions from bundled core.yml.
+
+    Returns
+    -------
+    core_variables : dict
+        Core variables that are always included.
+    flight_attitude : dict
+        Optional flight attitude variables (heading, pitch, roll).
+    derived_thermo : dict
+        Optional derived thermodynamic variables.
+    """
+    from importlib import resources
+
+    core_file = str(resources.files("glide").joinpath("assets/core.yml"))
+
+    with open(core_file) as f:
+        docs = [doc for doc in safe_load_all(f)]
+
+    core_variables = docs[0] if docs else {}
+    flight_attitude = docs[1] if len(docs) > 1 else {}
+    derived_thermo = docs[2] if len(docs) > 2 else {}
+
+    return core_variables, flight_attitude, derived_thermo
+
+
+def _apply_qc_overrides(variables: dict, qc_overrides: dict) -> dict:
+    """Apply QC parameter overrides to variable definitions.
+
+    Only allows overriding: valid_min, valid_max, max_gap, interpolate_missing
+    """
+    allowed_keys = {"valid_min", "valid_max", "max_gap", "interpolate_missing"}
+
+    for var_name, overrides in qc_overrides.items():
+        if var_name not in variables:
+            _log.warning("QC override for unknown variable: %s", var_name)
+            continue
+
+        for key, value in overrides.items():
+            if key not in allowed_keys:
+                _log.warning(
+                    "Ignoring invalid QC override key '%s' for %s", key, var_name
+                )
+                continue
+
+            # valid_min/max go in CF attributes
+            if key in ("valid_min", "valid_max"):
+                if "CF" not in variables[var_name]:
+                    variables[var_name]["CF"] = {}
+                variables[var_name]["CF"][key] = value
+                _log.debug("Override %s.CF.%s = %s", var_name, key, value)
+            else:
+                variables[var_name][key] = value
+                _log.debug("Override %s.%s = %s", var_name, key, value)
+
+    return variables
+
+
+def _build_slocum_name_map(variables: dict) -> dict:
+    """Build mapping from Slocum variable names to output variable names."""
+    slocum_name_map = {}
+    for variable_name, specs in variables.items():
+        if "source" not in specs:
+            continue
+        sources = specs["source"]
+        if not isinstance(sources, list):
+            sources = [sources]
+        for source in sources:
+            slocum_name_map[source] = variable_name
+
+    _log.debug("Slocum name mapping dict %s", slocum_name_map)
+    return slocum_name_map
+
+
 # Public functions
 
 
 def load_config(file: str | None = None) -> dict:
-    """Extract variable specifications from a yaml file."""
+    """Load and merge configuration from core and user files.
+
+    Parameters
+    ----------
+    file : str, optional
+        Path to user configuration file. If None, uses bundled default.
+
+    Returns
+    -------
+    dict
+        Merged configuration with keys:
+        - globals: trajectory and netcdf_attributes
+        - variables: all variable definitions (core + optional + user)
+        - slocum: mapping from Slocum names to output names
+        - merged_variables: variables for higher-level processing
+    """
+    # Load core definitions
+    core_variables, flight_attitude, derived_thermo = _load_core()
+
+    # Load user config
     if file is None:
         from importlib import resources
 
@@ -27,30 +132,67 @@ def load_config(file: str | None = None) -> dict:
     with open(file) as f:
         docs = [doc for doc in safe_load_all(f)]
 
-    global_config = docs[0]
-    variable_specs = docs[1]
-
-    slocum_name_map = {
-        source: variable_name
-        for variable_name, specs in variable_specs.items()
-        if "source" in specs
-        for source in (
-            specs["source"] if isinstance(specs["source"], list) else [specs["source"]]
-        )
-    }
-
-    _log.debug("Slocum name mapping dict %s", slocum_name_map)
-
-    # pyyaml loads datetime objects in local timezone as datetime.datetime objects.
-    # We need to ensure that all datetime objects are in UTC timestamps for processing to work.
-    for attr in ["valid_min", "valid_max"]:
-        if attr in variable_specs["time"]["CF"]:
-            variable_specs["time"]["CF"][attr] = _ensure_utc(
-                variable_specs["time"]["CF"][attr]
-            ).timestamp()
+    # Parse user config documents
+    global_config = docs[0] if docs else {}
+    include_config = docs[1] if len(docs) > 1 else {}
+    qc_config = docs[2] if len(docs) > 2 else {}
+    l1_variables = docs[3] if len(docs) > 3 else {}
+    merged_variables = docs[4] if len(docs) > 4 else {}
+
+    # Extract include toggles (default to True for backward compatibility)
+    include = include_config.get("include", {})
+    include_flight = include.get("flight_attitude", True)
+    include_thermo = include.get("derived_thermo", True)
+
+    # Build variable set: start with core
+    variables = copy.deepcopy(core_variables)
+
+    # Add optional suites if enabled
+    if include_flight:
+        variables.update(copy.deepcopy(flight_attitude))
+        _log.debug("Including flight_attitude suite")
+    if include_thermo:
+        variables.update(copy.deepcopy(derived_thermo))
+        _log.debug("Including derived_thermo suite")
+
+    # Apply QC overrides
+    qc_overrides = qc_config.get("qc", {}) if isinstance(qc_config, dict) else {}
+    variables = _apply_qc_overrides(variables, qc_overrides)
+
+    # Add user L1 variables
+    l1_vars = (
+        l1_variables.get("l1_variables", {}) if isinstance(l1_variables, dict) else {}
+    )
+    for var_name, var_spec in l1_vars.items():
+        if var_name in variables:
+            _log.warning("L1 variable '%s' conflicts with core variable", var_name)
+        else:
+            variables[var_name] = var_spec
+            _log.debug("Added L1 variable: %s", var_name)
+
+    # Build Slocum name mapping
+    slocum_name_map = _build_slocum_name_map(variables)
+
+    # Handle time valid_min/max UTC conversion
+    if "time" in variables and "CF" in variables["time"]:
+        for attr in ["valid_min", "valid_max"]:
+            if attr in variables["time"]["CF"]:
+                val = variables["time"]["CF"][attr]
+                if isinstance(val, datetime):
+                    variables["time"]["CF"][attr] = _ensure_utc(val).timestamp()
+
+    # Extract merged variables
+    merged_vars = (
+        merged_variables.get("merged_variables", {})
+        if isinstance(merged_variables, dict)
+        else {}
+    )
 
     config = dict(
-        globals=global_config, variables=variable_specs, slocum=slocum_name_map
+        globals=global_config,
+        variables=variables,
+        slocum=slocum_name_map,
+        merged_variables=merged_vars,
     )
 
     return config